@article {pmid41033070,
year = {2025},
author = {Han, M and Chen, Q and Li, Z and Hu, X and Ma, J and Qin, C and Gao, Y},
title = {Cellular mechanism of perfluoroalkyl substances with different chain lengths influence conjugative transfer of antibiotic resistance genes.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109810},
doi = {10.1016/j.envint.2025.109810},
pmid = {41033070},
issn = {1873-6750},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are emerging persistent environmental pollutants with potential risks to microbial ecosystems. However, the influence of PFAS with different chain lengths on horizontal gene transfer, particularly plasmid-mediated antibiotic resistance genes (ARGs) conjugation, remains poorly understood. This study investigated the impacts of short-chain (PFBA, PFHxA) and long-chain (PFNA) PFAS exhibited dual effects on the conjugative transfer of ARGs: PFAS with lower concentration (<0.05 mg/L) enhanced ARGs transfer by increasing the permeability of the cell membrane and ROS content, while higher concentration (>0.05 mg/L) of PFAS led to stronger inhibition through suppressing adenosine triphosphate (ATP) production. The scarcity of ATP caused cells to rebuild their energy allocation strategies, diverting more energy towards maintaining vital life activities rather than for gene transmission. Notably, short-chain PFAS (e.g. PFBA) of smaller molecular possessed greater facility for entering cells and caused stronger dual effects on cells. However, long-chain PFAS with high hydrophobicity prefers to embed in the phospholipid bilayer, causing weaker dual effects on cells and less frequency of conjugative transfer. These findings revealed the distinct effects of PFAS with different chain lengths on the conjugative transfer of ARGs, and highlighted the critical role of the cell membrane in this phenomenon. This research provides critical insights into the ecological risks posed by PFAS.},
}

@article {pmid41031813,
year = {2025},
author = {Mavrodi, DV and Blankenfeldt, W and Mavrodi, OV and Weller, DM and Thomashow, LS},
title = {Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0014723},
doi = {10.1128/mmbr.00147-23},
pmid = {41031813},
issn = {1098-5557},
abstract = {SUMMARYPhenazines are small, redox-active secondary metabolites produced by various bacterial species. These compounds participate in electron-transfer reactions, aiding microbes in surviving stressful or oxygen-limited environments. In this review, we examine the extensive structural diversity of phenazines and trace the evolutionary history of their biosynthetic pathways, which often move between distantly related species through horizontal gene transfer. We also explore how environmental factors such as nutrient levels and cell-to-cell signaling regulate phenazine production. Beyond their roles in microbial physiology, phenazines influence interactions among organisms, acting as antimicrobial agents, signaling molecules, and factors that shape microbiome dynamics in soils, plant roots, and other habitats. A better understanding of phenazine biology reveals how microbes adapt and thrive in diverse environments and emphasizes the potential applications of these compounds in agriculture and human health.},
}

@article {pmid41030841,
year = {2025},
author = {Anueyiagu, KN and Agusi, ER and Kabantiyok, D and Ayanbimpe, GM and Ikeh, EI},
title = {Zoonotic potential of ESBL-producing coliforms in pastorally managed ruminants with subclinical mastitis in Plateau State, Nigeria.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1632264},
pmid = {41030841},
issn = {2813-2467},
abstract = {BACKGROUND: Environmental coliform bacteria are frequently the cause of subclinical mastitis (SCM), a serious health issue in the dairy industry. Extended-spectrum β-lactamase (ESBL)-producing coliforms in livestock are a serious public health concern, particularly in environments where people and animals coexist. With an emphasis on their zoonotic and One Health implications, this study sought to evaluate the incidence of SCM and the occurrence of ESBL-producing coliforms in ruminants in Plateau State, Nigeria.

METHODS: The California Mastitis Test (CMT) was used to screen 287 milk samples that were taken from cows, ewes, and does. Standard microbiological methods were used to identify the bacterial isolates from CMT-positive samples. The presence of resistance genes (bla TEM and bla CTX-M) was ascertained by PCR, and ESBL production was confirmed phenotypically. Phylogenetic analysis showed genetic diversity and possible horizontal gene transfer among isolates.

RESULTS: Out of 287 milk samples, 79 (27.5%) had subclinical mastitis through the CMT, with a higher prevalence recorded in does 18(22.8%) while ewes and cows recorded 23(29.1%), and 38(48.1%) respectively. Of the 79 CMT-positive samples, the following isolates were identified: Citrobacter freundii (6.3%), Klebsiella pneumoniae (21.6%), K. oxytoca (2.5%), K. aerogenes (6.3%), and E. coli, being the most prevalent in cows (71%). Through PCR, 46 isolates expressed two important ESBL genes, bla TEM and bla CTX-M.

CONCLUSION: A possible zoonotic reservoir for antibiotic resistance in Nigeria is highlighted by the increased frequency of ESBL-producing coliforms in ruminants with SCM. These results highlight the necessity of implementing integrated One Health initiatives, such as public education, surveillance, and antimicrobial stewardship, in order to reduce the risk of resistant pathogen transmission from animals to people.},
}

@article {pmid41030195,
year = {2025},
author = {Vancaester, E and Oldrieve, GR and Reid, A and Koutsovoulos, G and Laetsch, DR and Makepeace, BL and Tanya, V and Poppert, S and Krücken, J and Wolstenholme, A and Blaxter, M},
title = {Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf226},
pmid = {41030195},
issn = {2160-1836},
abstract = {Many, but not all, parasitic filarial nematodes (Onchocercidae) carry intracellular, maternally-transmitted, alphaproteobacterial Wolbachia symbionts. The association between filarial nematodes and Wolbachia is often portrayed as mutualist, where the nematode is reliant on Wolbachia for an essential but unknown service. Wolbachia are targets for anti-filarial chemotherapeutic interventions for human disease. Wolbachia of Onchocercidae derive from four of the major supergroups (C, D, F and J) defined within the genus. We explored the evolutionary history of the filarial nematode-Wolbachia symbiosis in twenty-two nematode species, sixteen of which have current Wolbachia infections, by screening the nematode nuclear genome sequences for nuclear Wolbachia transfers, fragments of the Wolbachia genome that have been inserted into the nuclear genome. We identified Wolbachia insertions in five of the six species that have no current Wolbachia infection, showing they have previously had and have now lost Wolbachia infections. In currently-infected species we found a diversity of origins of the insertions, including many cases where they derived from a different supergroup to the current live infection. Mapping the origins of the insertions onto the filarial nematode phylogeny we derive a complex model of evolution of Wolbachia symbiosis. The history of association between Wolbachia and onchocercid nematodes includes not only cospeciation, as would be expected from a mutualist symbiosis, but also loss (in the five Wolbachia-free species), frequent symbiont replacement, and dual infection. This dynamic pattern is challenging to models that assume host-symbiont mutualism.},
}

@article {pmid41026744,
year = {2025},
author = {Disastra, Y and Wongsurawat, T and Jenjaroenpun, P and Hampson, DJ and Kamwa, R and Prapasarakul, N},
title = {Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332506},
pmid = {41026744},
issn = {1932-6203},
mesh = {*Probiotics/adverse effects ; *Pediococcus acidilactici/genetics/drug effects/pathogenicity ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Plasmids/genetics ; Genomics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Animals ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The increasing use of probiotics in livestock necessitates rigorous safety assessments to mitigate risks such as their inadvertent contribution to antimicrobial resistance (AMR) and horizontal gene transfer (HGT). This study employs whole-genome sequencing using both long-read (GridION, Oxford Nanopore Technologies) and short-read (Illumina, San Diego, CA, USA) platforms to assess the genomic and plasmidome profiles of five Thai strains of Pediococcus acidilactici, that previously have been evaluated for probiotic potential in livestock. Our comprehensive analysis identified genes encoding AMR, virulence factors, and probiotic-related genes. Notably, strains AF2519 and AF2019 harbored plasmid-borne tet(M) and erm(B) genes, with tet(M) embedded in a novel composite genetic arrangement flanked by mobile elements, suggesting historical recombination and altered mobility potential. Strains IAF6519, IAF5919, and P72N, free from plasmid-borne AMR genes, emerged as safer candidates, lacking virulence genes. Phenotypic tests revealed discrepancies with genomic data; for instance, AF2019 was resistant to clindamycin without detectable genes, and showed susceptibility to tetracycline despite the presence of tet(M). The absence of complete transfer machinery in AF2519 and AF2019 suggests a reduced HGT risk. These findings underscore the importance of integrating genomic and phenotypic approaches in probiotic safety evaluations. The presence of plasmid-borne AMR genes in certain strains advises caution in their use, impacting probiotic selection and regulatory compliance in agriculture. This research informs policies and best practices for safe probiotic deployment, ensuring both efficacy and safety.},
}

*Probiotics/adverse effects
*Pediococcus acidilactici/genetics/drug effects/pathogenicity
*Genome, Bacterial
Gene Transfer, Horizontal
Plasmids/genetics
Genomics
Virulence Factors/genetics
Whole Genome Sequencing
Animals
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid41025674,
year = {2025},
author = {Ste-Croix, DT and Gagnon, AÈ and Mimee, B},
title = {The genome and stage-specific transcriptomes of the carrot weevil, Listronotus oregonensis, reveal adaptive mechanisms for host specialisation and symbiotic interactions.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70012},
pmid = {41025674},
issn = {1365-2583},
support = {J-002846//Alternative Pest Management Solutions initiative/ ; //Agriculture and Agri-Food Canada/ ; },
abstract = {Throughout their evolution, insects have become specialised to occupy diverse ecological niches. The carrot weevil, Listronotus oregonensis, is an important agricultural pest that exhibits a very specific host range. In this study, we characterised the genome and transcriptomes of each developmental stage of L. oregonensis and its Wolbachia endosymbiont to gain deeper knowledge of the genetic determinants controlling its biology. We annotated 14,637 genes and showed expression profiles across the developmental stages. We also compared orthologous genes between L. oregonensis and nine other species, with particular focus on chemoreceptors and detoxification genes. We identified 24 distinct odorant-binding protein genes and 41 genes for receptors involved in stimulus perception, relatively low numbers compared with other species, which would be consistent with a narrow host range. In contrast, we found a high number of detoxification genes, with significant expansion of certain gene families. Among the annotated genes, 46 were putatively acquired through horizontal gene transfer, with 17 showing strong evidence for this, including several cell-wall degrading enzymes. The phylogeny of a cytolethal distending toxin gene also suggests an initial transfer from a prokaryotic source and vertical dissemination in members of Curculionidae through recent evolution. The presence of the endosymbiotic bacterium Wolbachia (supergroup A) was confirmed in all tested L. oregonensis individuals from several regions in northeastern North America and showed very little diversity. This study enhances our understanding of the genomic, functional, and evolutionary aspects of a significant agricultural pest and makes important and useful databases available to the scientific community.},
}

@article {pmid41025482,
year = {2025},
author = {Karan, R and Pyne, A and Panda, SK and Sen Gupta, PS and Hazra, S},
title = {Mechanistic insights into ESBL activity of subclass A2 in Class A beta-lactamase revealing a distinct strategy towards conferring drug resistance.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/07391102.2025.2563080},
pmid = {41025482},
issn = {1538-0254},
abstract = {The twenty first century has witnessed challenges with antimicrobial resistance (AMR) emerging as a critical global threat. Among its most concerning is antibiotic resistance (ABR), highly linked to beta-lactamases. Among others, Class A beta-lactamases, present significantly with functional diversity, although ESBLs are one of the major concerns. A key defence mechanism in Gram-negative bacteria is the overexpression of ESBLs (Extended spectrum beta-lactamases) which spread across the bacterial population through horizontal gene transfer causes serious nosocomial infections. Since ESBLs have developed to increase their substrate specificity and hydrolyse most cephalosporins, penicillins, and monobactams, research into them is urgently needed.However, despite attempts functional classification, based on sequence identity, fold similarity, the presence or absence of insertions, particularly in loop regions and mode of action, a universally accepted framework remains elusive. Previous studies have broadly categorized Class A beta-lactamases into subclasses A1 and A2, yet the mechanistic intricacies of subclass A2 only as ESBL demand a more nuanced, multilevel analysis, underlying their role in antibiotic resistance. To bridge this knowledge gap, we employed on a comprehensive investigation encompassing sequence, structure, molecular docking, and dynamic analyses to elucidate the mechanistic approach of antibiotic resistance profiles for these two subclasses. Our sequence and structural studies revealed differences, particularly in insertions, structural alignments, and loop regions, including the omega loop and loops near the active site. Molecular docking study demonstrated better binding of the bigger substrate in the active site cavity of A2 subclass representatives. Dynamic analyses further confirmed our findings, employing root mean square deviation (RMSD), root mean square fluctuation (RMSF), flexibility of the extended and omega loops, radius of gyration (Rg), solvent-accessible surface area (SASA), clustering, hydrogen bonding patterns, principal component analysis (PCA), and free energy landscape (FEL). This study provides insights into the molecular distinctions and resistance mechanisms of these subclasses, paving the way for advanced research in antibiotic resistance and strengthening novel therapeutic strategies.},
}

@article {pmid41024490,
year = {2025},
author = {Speijer, D},
title = {Eukaryogenesis From FECA to LECA: Radical Steps Along the Way.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70063},
doi = {10.1002/bies.70063},
pmid = {41024490},
issn = {1521-1878},
abstract = {The characteristics of the last eukaryotic common ancestor (LECA) population and the root of the eukaryotic tree have been coming into focus lately. However, the trajectory taking the host, related to present-day Asgard archaea and the endosymbiont, related to present-day alphaproteobacteria, toward such fully integrated and complex organisms is still unclear. Here I marshal recent evidence supporting the early arrival of the "mitochondrion-to-be", setting up the evolutionary dynamic for a series of mutual adaptations leading to eukaryotes. Upon critical analysis of some presuppositions in phylogenomic reconstructions of eukaryogenesis, I again propose that pre-symbiosis, efficient ATP generation, internal reactive oxygen species (ROS) formation and enhanced retention of genes supplied by horizontal gene transfer (HGT) interdependently allowed this unique transformation to occur.},
}

@article {pmid41023737,
year = {2025},
author = {Dandare, SU and Allenby, A and Silvano, E and Nockemann, P and Chen, Y and Smith, TJ and Kumaresan, D},
title = {Diversity and distribution of the lanthanome in aerobic methane-oxidising bacteria.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {120},
pmid = {41023737},
issn = {2524-6372},
support = {NE/X005119//UK Research and Innovation/ ; NE/X005062//UK Research and Innovation/ ; },
abstract = {BACKGROUND: Lanthanides (Ln) play important and often regulatory roles in the metabolism of methylotrophs, including methanotrophs, particularly through their involvement in methanol oxidation. However, the diversity, distribution, and ecological relevance of Ln-associated proteins (the lanthanome) in aerobic methane-oxidising bacteria (MOB) remain underexplored. This study investigates the lanthanome using genome, plasmid, and proteome data, alongside metatranscriptome data from methane-rich lake sediments.

RESULTS: We surveyed 179 genomes spanning Proteobacterial, Verrucomicrobial, and Actinobacterial MOBs to examine the distribution of Ln-dependent methanol dehydrogenases (MDHs) and Ln transport proteins. Distinct lineage-specific patterns were observed: XoxF5 was the most widespread MDH variant in Proteobacteria, while XoxF2 was restricted to Verrucomicrobia. Transporter systems also showed distinct patterns, with LanM restricted to Alphaproteobacteria, LanPepSY and LanA confined to Gammaproteobacteria, and LutH-like receptors broadly distributed across all lineages. Homologues of these genes were also detected on plasmids, indicating potential for horizontal gene transfer. In Lake Washington sediment metatranscriptomes, lanthanome transcripts were detected, with Proteobacteria as dominant contributors. Notably, a large fraction of xoxF transcripts were affiliated with non-MOB Methylophilaceae, consistent with known cooperative interactions with MOB. Using Methylosinus trichosporium OB3b as a model, we assessed methane oxidation and proteomic responses to soluble CeCl3 and a mixed-lanthanide ore. Lag phases were prolonged in the presence of lanthanides, particularly with ore, but methane oxidation rates converged across treatments after acclimation. Proteomic analysis revealed extensive condition-specific responses, with 724 proteins differentially expressed in Ore treatment compared to 60 under CeCl3. XoxF3 and XoxF5 were upregulated while MxaF and its accessory proteins were downregulated, consistent with the "lanthanide switch". Notably, LanM was not expressed despite being encoded, whereas LutH-like receptor was downregulated under both treatments, likely reflecting regulatory control to prevent excess metal uptake. Additional upregulation of a TonB-dependent receptor and ABC transporter suggests a potential lanthanophore-mediated uptake strategy.

CONCLUSION: This study highlights the diversity and ecological activity of Ln-binding and transport systems in MOBs, their plasmid localisation and potential mobility, and their distinct regulation under different Ln sources. The strong proteomic response to complex ore underscores the physiological flexibility of MOBs in coping with natural lanthanide forms. These findings provide a framework for ecological studies and candidate targets for biotechnological applications in methane bioconversion and sustainable lanthanide recovery from complex materials.},
}

@article {pmid41022706,
year = {2025},
author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE},
title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8559},
pmid = {41022706},
issn = {2041-1723},
support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; },
mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; },
abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.},
}

Phylogeny
*Haptophyta/genetics/classification/metabolism
Phylogeography
Gene Transfer, Horizontal
Metagenome
Oceans and Seas
Genome
Genomics

@article {pmid41022263,
year = {2025},
author = {Zhang, J and Liu, Y and Fang, L and Wang, X and Xu, H and Lou, D},
title = {Molecular Characterization of blaVIM-2-carrying Pseudomonas asiatica L2126: Identification of a ∼44 kb Untypable Plasmid with Intra-Genus Dissemination Potential.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.012},
pmid = {41022263},
issn = {2213-7173},
abstract = {OBJECTIVES: This study aims to elucidate the molecular characteristics of a blaVIM-2-carrying Pseudomonas asiatica isolate (L2126) from China and to characterize a ∼44 kb untypable plasmid harboring blaVIM-2. We investigated the genetic context of blaVIM-2, assessed the associated antimicrobial resistance determinants, and explored the role of this plasmid in mediating gene dissemination.

METHODS: The isolate L2126 was recovered from an intestinal colonization sample in a patient from Hangzhou, China. Species identification was confirmed by average nucleotide identity (ANI) analysis. Hybrid whole-genome sequencing was performed using Illumina short-read and Oxford Nanopore long-read platforms. Genome assembly was conducted using Unicycler and annotated with Prokka. Antimicrobial resistance genes were identified via ResFinder and CARD. The genetic context of blaVIM-2 was delineated using IntegronFinder. Plasmid profiles were determined by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and in silico replicon analysis.

RESULTS: L2126 exhibited a multidrug-resistant profile with high-level resistance to carbapenems, cephalosporins, and fluoroquinolones. Genome analysis revealed 7 resistance genes, including blaVIM-2 and sul1. Notably, blaVIM-2 resides within a class 1 integron (intI1-attI1- blaVIM-2-qacEΔ1-sul1) embedded in a Tn402-like platform on a ∼44 kb untypable plasmid. The adjacent tni module (tniR-tniQ-tniB-tniA) is encoded on the opposite strand, indicating that it is part of the transposition platform rather than the integron cassette array. S1-PFGE confirmed the presence of the ∼44 kb plasmid, and in silico analysis provided a schematic representation of its genetic organization. BLAST analysis demonstrated that this plasmid shares high sequence homology with a plasmid previously identified in Pseudomonas monteilii, despite the two isolates belonging to different species.

CONCLUSIONS: Our findings demonstrate that the carriage of blaVIM-2 on a novel ∼44 kb untypable plasmid in P. asiatica L2126 could facilitate horizontal gene transfer of carbapenem resistance. The plasmid's high homology to one previously identified in P. monteilii suggests that it has the potential for intra-genus dissemination, posing a significant threat to the spread of carbapenem resistance.},
}

@article {pmid41021386,
year = {2025},
author = {Dechêne-Tempier, M and Bougeard, S and Loux, V and Chiapello, H and Libante, V and Marois-Créhan, C and Leblond-Bourget, N and Payot, S},
title = {Pan-immune system, mobilome and resistome in Streptococcus suis.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001521},
pmid = {41021386},
issn = {2057-5858},
mesh = {*Streptococcus suis/genetics/immunology/drug effects ; *Interspersed Repetitive Sequences ; Phylogeny ; Genome, Bacterial ; Swine ; Animals ; Gene Transfer, Horizontal ; Streptococcal Infections/microbiology ; *Drug Resistance, Bacterial/genetics ; Swine Diseases/microbiology ; },
abstract = {Streptococcus suis is a bacterial pathogen responsible for infections in pigs and in wild fauna that can also lead to severe infections in humans. Increasing antimicrobial resistance (AMR) has been described for this zoonotic pathogen worldwide. Since most of these AMR genes are carried by mobile genetic elements (MGEs), they can largely disseminate by horizontal gene transfer. Taking advantage of the large set of genomes available for this species, an exhaustive search of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) was undertaken in a representative set of 400 selected high-quality genomes of S. suis. We examined how these elements vary across phylogenetic clades and ecotypes and their association with AMR genes and defence systems (DSs), including restriction-modification (RM), CRISPR and also less studied DSs. This investigation identified 569 ICEs, belonging to the 7 families previously described in streptococci, inserted in 12 distinct specific integration sites. Additionally, 1,035 IMEs characterized by 11 distinct relaxase families and integrated in 10 specific chromosomal sites were detected in the 400 genomes of S. suis. New associations between ICE/IME and AMR genes were discovered. A huge diversity of putative DSs was observed including 2,035 RM systems, 124 CRISPR systems and systems belonging to 20 other categories, most of them described as efficient against phages and plasmids. Furthermore, most of the spacers associated with CRISPR systems target these MGEs rather than integrative elements. In addition, many integrative elements appear to carry an orphan methylase that could help them escape RM systems. Altogether, this points out that ICEs and IMEs are spared by DSs and play a major role in AMR dissemination in S. suis. In addition, most of the strains have the full set of genes required for competence, i.e. for the acquisition of extracellular DNA by natural transformation. This suggests a high risk of AMR dissemination in S. suis.},
}

*Streptococcus suis/genetics/immunology/drug effects
*Interspersed Repetitive Sequences
Phylogeny
Genome, Bacterial
Swine
Animals
Gene Transfer, Horizontal
Streptococcal Infections/microbiology
*Drug Resistance, Bacterial/genetics
Swine Diseases/microbiology

@article {pmid41020918,
year = {2025},
author = {Kunarisasi, S and Yuliandari, P and Pramono, AK and Furqoni, AH and Aliyah, SH and Nurjannah, I and Thaiyibah, N and Pratama, R and Permata Sari, NI},
title = {Genomic characterization of multidrug-resistant Escherichia coli isolates from hospital wastewater in Jakarta, Indonesia.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {960},
pmid = {41020918},
issn = {1573-4978},
support = {UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; },
mesh = {*Wastewater/microbiology ; Indonesia ; *Escherichia coli/genetics/isolation & purification/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing/methods ; Hospitals ; Phylogeny ; Virulence Factors/genetics ; Plasmids/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; Humans ; Anti-Bacterial Agents/pharmacology ; High-Throughput Nucleotide Sequencing/methods ; Microbial Sensitivity Tests ; Virulence/genetics ; },
abstract = {BACKGROUND: Hospital wastewater is a reservoir of antimicrobial resistance (AMR), yet the genetic diversity and resistance mechanisms of environmental Escherichia coli in such settings remain underexplored. This study aimed to investigate the genomic characteristics, resistance profiles, and virulence potential of E. coli isolates recovered from a hospital wastewater in Jakarta, Indonesia.

METHODS AND RESULTS: Six Escherichia coli isolates from hospital wastewater were sequenced using short-read next-generation sequencing (NGS). Raw reads were quality-checked and assembled with SPAdes, with five genomes retained for downstream analysis. Antimicrobial resistance (AMR) genes were identified using Staramr and the CARD database, while virulence factors were predicted using Abricate against the Virulence Factors Database (VFDB). Plasmid replicons were detected with PlasmidFinder. Phylogroup assignment followed the Clermont typing method, and phylogenetic analysis was conducted using a neighbor-joining tree based on core genome MLST (cgMLST) generated with chewBBACA v3.3.10. Multilocus sequence typing (MLST) revealed five distinct sequence types (ST744, ST156, ST1196, ST38, and ST10) across three phylogroups (A, B1, and D). A total of 57 AMR genes were detected, including blaCTX-M-15, blaCMY-2, and blaOXA-1 along with plasmid-mediated and chromosomal mutations conferring resistance to fluoroquinolones, aminoglycosides, and tetracyclines.

CONCLUSIONS: E. coli from hospital wastewater in Jakarta exhibited high genomic diversity, multidrug resistance, and variable virulence profiles. The findings support the role of untreated hospital effluents as a hotspot for AMR emergence and horizontal gene transfer. This showed the need for routine environmental surveillance to mitigate the public health risks associated with environmental reservoirs of resistant pathogens.},
}

*Wastewater/microbiology
Indonesia
*Escherichia coli/genetics/isolation & purification/drug effects/pathogenicity
*Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing/methods
Hospitals
Phylogeny
Virulence Factors/genetics
Plasmids/genetics
Genome, Bacterial/genetics
Genomics/methods
Humans
Anti-Bacterial Agents/pharmacology
High-Throughput Nucleotide Sequencing/methods
Microbial Sensitivity Tests
Virulence/genetics

@article {pmid41020186,
year = {2025},
author = {Kleyn, MS and Akinyemi, MO and Bezuidenhout, C and Adeleke, R},
title = {Draft genome sequence of Lysinibacillus capsici NAVL5D with potential for plant growth promotion.},
journal = {3 Biotech},
volume = {15},
number = {10},
pages = {359},
pmid = {41020186},
issn = {2190-572X},
abstract = {UNLABELLED: The use of plant growth-promoting (PGP) bacteria is an emerging strategy for sustainable agriculture, offering alternatives to chemical fertilisers and pesticides. Here, we report the draft genome sequence and functional characterization of Lysinibacillus capsici NAVL5D isolated from the leaf of ready-to-eat lettuce plant grown in South Africa. The genome generated using the Illumina NovaSeq 6000 had a size of 4,631,824 bp, with 22 contigs and a G + C content of 37.3%. In vitro tests demonstrated the strain's potential for plant growth promotion through nitrogen fixation, phosphate solubilization, indole-3-acetic acid (IAA) production, hydrogen cyanide (HCN) synthesis, and siderophore production. Genome analysis revealed key subsystems underpinning these traits such as auxin biosynthesis, nitrogen, phosphorus, and potassium metabolism, as well as putative PGP genes supporting these growth-promoting traits. In addition, five biocontrol secondary metabolites were predicted in the genome including terpenes and cyclic-lactone-autoinducers. However, eight minimal pathogenicity-related genes and six antibiotic resistance genes were also identified, including vanW, vanT, vanY, qacJ, msr(G), and FosBx1. Antibiotic susceptibility testing confirmed resistance to beta-lactams. Evidence of phage with could mediate horizontal gene transfer was observed in the genome. In vivo seed germination assays further demonstrated the strain's ability to promote plant growth, confirming its functional potential beyond in vitro observations. While L. capsici NAVL5D shows promise for sustainable agriculture applications, its potential warrant further investigation to ensure its safe use as a plant growth-promoting agent.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04488-y.},
}

@article {pmid41019531,
year = {2025},
author = {Bhat, BA and Mir, RA and Qadri, H and Dhiman, R and Almilaibary, A and Alkhanani, M and Mir, MA},
title = {Correction: Integrons in the development of antimicrobial resistance: critical review and perspectives.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1681413},
doi = {10.3389/fmicb.2025.1681413},
pmid = {41019531},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1231938.].},
}

@article {pmid41016251,
year = {2025},
author = {Schubert, K and Shosanya, T and García-Bayona, L},
title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102675},
doi = {10.1016/j.mib.2025.102675},
pmid = {41016251},
issn = {1879-0364},
abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.},
}

@article {pmid41016209,
year = {2025},
author = {Zhao, Q and Yu, C and Liu, X and Hu, X and Yang, Q},
title = {Multi-omics reveals the systematical influence of composite heavy metal(loid)s on soil microbial function: Elemental cycling and microbial adaptation mechanisms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139973},
doi = {10.1016/j.jhazmat.2025.139973},
pmid = {41016209},
issn = {1873-3336},
abstract = {As the core of soil material cycling, soil microecosystems contaminated by combined heavy metal(loid)s have attracted widespread concern. Previous studies mostly focused on community-level ecological functions, neglecting genomic-level investigations and comprehensive microbial adaptation mechanisms. Here, we integrated multi-omics (metagenomics, genome assemblies, comparative genomics) with field and lab studies to explore responses from community to genomic scales. We found that metal(loid)s altered the assembly of microbial functional genes and weakened functional networks linking carbon, nitrogen, phosphorus, and sulfur cycling. They reduced the potential of carbohydrate metabolism, carbon fixation, and sulfur metabolism involved in protein synthesis and disrupted normal organic matter decomposition (via certain CAZymes). Conversely, they increased the potential of methanogenesis, denitrification, and organic phosphorus mineralization, as well as stimulating dissimilatory sulfate reduction and sulfur disproportionation. Microbes employed multi-level strategies to combat persistent heavy metal(loid)s stress, including reducing metal ion uptake, facilitating intracellular detoxification, and activating efflux pathways. They underwent adaptive evolution through mechanisms such as enhancing the synthesis and transportation of siderophores, strengthening DNA damage repair, and promoting genome streamlining. Notably, our analysis revealed that horizontal gene transfer, mediated by mobile genetic elements, drives the acquisition of resistance genes. This study provides systematic genomic evidence for such adaptive mechanisms in functional microbes, greatly advancing our understanding of their bioremediation potential.},
}

@article {pmid41015591,
year = {2025},
author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A},
title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41015591},
issn = {1432-1912},
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.},
}

@article {pmid41014670,
year = {2025},
author = {Liu, W and Gong, F and Huang, Y and Shao, Y and Wang, Z and Xiao, X},
title = {Acetylshikonin regulates the gut microbiota and inhibits the horizontal transmission of colistin-resistant plasmids.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157287},
doi = {10.1016/j.phymed.2025.157287},
pmid = {41014670},
issn = {1618-095X},
abstract = {BACKGROUND: The gut microbiota serves as a major reservoir for antibiotic resistance genes (ARGs), driving the spread of antimicrobial resistance (AMR) via horizontal gene transfer (HGT). Acetylshikonin (ASK), a naphthoquinone derived from the medicinal plant Lithospermum erythrorhizon, was proved to inhibit plasmid conjugation in vitro and in vivo. However, its impact on gut microbiota composition and precise HGT inhibition process within complex gut microbiota community remains unexplored.

PURPOSE: This study aims to clarify the precise inhibition effect of ASK on the transfer process of colistin-resistant plasmid in gut microbiota and its mechanisms.

METHODS: High-throughput cell sorting and 16S rRNA gene amplicon sequencing were employed to assess the precise gut microbiota species that ASK inhibited the resistant plasmid transfer to. The plasmid stability and re-transferability of transconjugants was evaluated by passaging culture and in vitro conjugative assay. The biochemical impact of ASK on donor cell and gut microbiota were tested by fluorescence assay and ELISA.

RESULTS: ASK changed the gut microbiota composition by enriching probiotics and reducing Gram-positive bacteria. In addition, ASK effectively inhibited the conjugative transfer of colistin-resistant plasmids to Proteobacteria (Escherichia and Ligilactobacillus) within the gut community. Furthermore, ASK weakened the stability and re-transferability of transconjugants, thereby limiting ARG further dissemination in gut. Moreover, ASK inhibited the electronic transport chain (ETC) and suppressed the ATP supply for both donor cells and the gut microbiota. Thus the plasmid conjugation processing in gut microbiota was inhibited by ASK.

CONCLUSION: This study demonstrated that ASK restructured gut microbiota and disarmed plasmid-mediated resistance spreading, offering a dual-targeted strategy against antimicrobial resistance.},
}

@article {pmid41013258,
year = {2025},
author = {Shelenkov, A and Slavokhotova, A and Yunusova, M and Kulikov, V and Mikhaylova, Y and Akimkin, V},
title = {Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Staphylococcus aureus.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {65},
pmid = {41013258},
issn = {2730-6844},
mesh = {*Virulence Factors/genetics ; *Plasmids/genetics ; *Staphylococcus aureus/genetics/classification/pathogenicity/drug effects ; *Replicon ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; *Databases, Genetic ; Humans ; Genomics ; Staphylococcal Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Bacterial infections pose a global health threat across clinical and community settings. Over the past decade, the alarming expansion of antimicrobial resistance (AMR) has progressively narrowed therapeutic options, particularly for healthcare-associated infections. This critical situation has been formally recognized by the World Health Organization as a major public health concern. Epidemiological studies have demonstrated that the dissemination of AMR is frequently mediated by specific high-risk bacterial lineages, often designated as "global clones" or "clonal complexes." Consequently, surveillance of these epidemic clones and elucidation of their pathogenic mechanisms and AMR acquisition pathways have become essential research priorities. The advent of whole genome sequencing has revolutionized these investigations, enabling comprehensive epidemiological tracking and detailed analysis of mobile genetic elements responsible for resistance gene transfer. However, despite the exponential increase in available bacterial genome sequences, significant challenges persist. Current genomic datasets often suffer from uneven representation of clinically relevant strains and inconsistent availability of accompanying metadata. These limitations create substantial obstacles for large-scale comparative studies and hinder effective surveillance efforts.

DESCRIPTION: This database represents a comprehensive genomic analysis of 98,950 Staphylococcus aureus isolates, a high-priority bacterial pathogen of global clinical significance. We provide detailed isolate characterization through several established typing schemes including multilocus sequence typing (MLST), clonal complex (CC) assignments, spa typing results, and core genome MLST (cgMLST) profiles. The dataset also documents the presence of CRISPR-Cas systems in these isolates. Beyond fundamental typing data, our resource incorporates the distribution of antimicrobial resistance determinants, virulence factors, and plasmid replicons. These systematically curated genomic features offer researchers valuable insights into isolate epidemiology, resistance mechanisms, and horizontal gene transfer patterns in this highly concerning pathogen.

CONCLUSION: This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.14833440 . The data provided enables researchers to identify optimal reference isolates for various genomic studies, supporting critical investigations into S. aureus epidemiology and antimicrobial resistance evolution. This resource will ultimately inform the development of more effective prevention and control measures against this high-priority pathogen.},
}

*Virulence Factors/genetics
*Plasmids/genetics
*Staphylococcus aureus/genetics/classification/pathogenicity/drug effects
*Replicon
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
*Databases, Genetic
Humans
Genomics
Staphylococcal Infections/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid41012719,
year = {2025},
author = {Hu, J and Zhou, J and Wang, L and Chen, Z and Tan, Y and Yin, Y and Pei, Z and Li, C and Bai, H and Ma, C and Teng, L and Feng, Y and Li, X and Wei, Y and Peng, H},
title = {Antimicrobial Resistance and Genomic Characterization of an Escherichia coli Strain Harboring p0111 and an IncX1-Type Plasmid, Isolated from the Brain of an Ostrich.},
journal = {Veterinary sciences},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/vetsci12090793},
pmid = {41012719},
issn = {2306-7381},
support = {AB231111//Hechi City Key Research and Development Program/ ; AB24002021//Fangchenggang City Key Research and Development Program/ ; 2024GXZCLK37//Guangxi Self-funded Forestry Science and Technology Project/ ; 4-14, 24-2, 24-10, 24-12//Guangxi Science and Technology Special Projects/ ; 202219; Z202218; Z202214//Guangxi Zhuang Autonomous Region Department of Agriculture and Rural Affairs Self-Funded Projects/ ; 20220136-5//Guilin City Technology Application and Promotion Program/ ; AB241484045, AB23075145//Guangxi Key Research and Development Program/ ; },
abstract = {An outbreak characterized by clinical signs of diarrhea and paralysis, occasionally progressing to fatal outcomes, occurred at an ostrich breeding facility. Conventional antibiotic treatments proved ineffective. To investigate the etiology of the disease, brain and liver specimens were collected for diagnostic analysis. An Escherichia coli (E. coli) isolate, designated strain HZDC01, was obtained from cerebral tissues, and whole-genome sequencing was performed for genomic characterization. Genomic analysis revealed that the chromosomal DNA harbors numerous resistance genes, conferring multidrug resistance through complex mechanisms. Furthermore, a p0111-type plasmid carrying the blaCTX-M-55 gene and an IncX1-type plasmid harboring rmtB, sul1, APH(6)-Id, tet(A), AAC(3)-IIc, aadA2, blaTEM-1B, and floR genes were identified. These plasmids carry numerous mobile genetic elements that can disseminate via horizontal gene transfer, thereby amplifying the risk of resistance-gene spread within bacterial populations. Additionally, the ibeB and ibeC genes, which encode proteins involved in the invasion of brain microvascular endothelial cells, were identified. These genes may facilitate E. coli penetration of the blood-brain barrier, potentially leading to meningitis and posing a life-threatening risk to the host. This is the first report of the isolation and characterization of extended-spectrum beta-lactamase E. coli from the brain of an ostrich with paralysis. The findings provide valuable genomic insights into the antimicrobial resistance profiles and pathogenic mechanisms of ostrich-derived E. coli isolates.},
}

@article {pmid41011463,
year = {2025},
author = {Tsolakidou, P and Chatzidimitriou, M},
title = {Epidemiological and Microbiological Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates in a Regional Greek Hospital: A Retrospective Study.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092132},
pmid = {41011463},
issn = {2076-2607},
abstract = {Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase phenotypes with clinical and epidemiological parameters. Demographic, clinical, and microbiological data were extracted from patient records, and isolates underwent phenotypic carbapenemase detection, antimicrobial susceptibility testing, and molecular characterization using real-time PCR; four isolates were further analyzed using whole-genome sequencing. CRKP was detected across multiple hospital departments, notably in the Emergency Department (n = 5) and Intensive Care Unit (n = 6). KPC producers predominated (n = 9), followed by NDM (n = 6), VIM (n = 1), and OXA-48 (n = 6). All VIM- or NDM + VIM-positive cases were associated with mortality. High-risk clones, including ST15, ST11, and ST307, were identified, with one ST15 isolate harboring blaNDM-1, blaVIM-1, and chromosomal colistin resistance; this is the first such report in Greece. Colistin and gentamicin were the most active agents in vitro; three isolates were pan-drug-resistant. The findings highlight significant CRKP circulation outside ICUs, the role of horizontal gene transfer in resistance dissemination, and the need to expand screening and rapid diagnostics to non-ICU settings. Enhanced molecular surveillance targeted at infection control and strengthened antimicrobial stewardship programs are essential for limiting the spread of CRKP.},
}

@article {pmid41011454,
year = {2025},
author = {Zhang, P and Mo, Q and Liu, C and Liu, Q and Xu, J and Wang, Y and Wen, X and Wu, Y},
title = {Dose-Dependent Effect of Tilmicosin Residues on ermA Rebound Mediated by IntI1 in Pig Manure Compost.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092123},
pmid = {41011454},
issn = {2076-2607},
support = {2023A1515110839//Guangdong Basic and Applied Basic Research Foundation/ ; 32172781//National Natural Science Foundation of China/ ; 2024M760976//China Postdoctoral Science Foundation/ ; 2023B0202060001//Key-Area Research and Development Program of Guangdong Province/ ; GZC20240507//Postdoctoral Fellowship Program of CPSF/ ; 2023B1212060057//Science and Technology Program of Guangdong province, China/ ; },
abstract = {The impact of varying antibiotic residue levels on antibiotic resistance gene (ARG) removal during composting is still unclear. This study investigated the impact of different residue levels of tilmicosin (TIM), a common veterinary macrolide antibiotic, on ARG removal during pig manure composting. Three groups were used: the CK group (no TIM), the L group (246.49 ± 22.83 mg/kg TIM), and the H group (529.99 ± 16.15 mg/kg TIM). Composting removed most targeted macrolide resistance genes (MRGs) like ereA, ermC, and ermF (>90% removal), and reduced ermB, ermX, ermQ, acrA, acrB, and mefA (30-70% removal). However, ermA increased in abundance. TIM altered compost community structure, driving succession through a deterministic process. At low doses, TIM reduced MRG-bacteria co-occurrence, with horizontal gene transfer via intI1 being the main cause of ermA rebound. In conclusion, composting reduces many MRG levels in pig manure, but the persistence and rebound of genes like ermA reveal the complex interactions between composting conditions and microbial gene transfer.},
}

@article {pmid41011444,
year = {2025},
author = {Li, Z and Tang, J and Wang, X and Ma, X and Yuan, H and Gao, C and Guo, Q and Guo, X and Wan, J and Dagot, C},
title = {The Environmental Lifecycle of Antibiotics and Resistance Genes: Transmission Mechanisms, Challenges, and Control Strategies.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092113},
pmid = {41011444},
issn = {2076-2607},
support = {241111321400//Henan Provincial Key Research and Development Special Project/ ; },
abstract = {Antibiotics are widely used in modern medicine. However, as global antibiotic consumption rises, environmental contamination with antibiotics and antibiotic resistance genes (ARGs) is becoming a serious concern. The impact of antibiotic use on human health is now under scrutiny, particularly regarding the emergence of antibiotic-resistant bacteria (ARB) in the environment. This has heightened interest in technologies for treating ARGs, highlighting the need for effective solutions. This review traces the life cycle of ARB and ARGs driven by human activity, revealing pathways from antibiotic use to human infection. We address the mechanisms enabling resistance in ARB during this process. Beyond intrinsic resistance, the primary cause of ARB resistance is the horizontal gene transfer (HGT) of ARGs. These genes exploit mobile genetic elements (MGEs) to spread via conjugation, transformation, transduction, and outer membrane vesicles (OMVs). Currently, biological wastewater treatment is the primary pollution control method due to its cost-effectiveness. However, these biological processes can promote ARG propagation, significantly amplifying the environmental threat posed by antibiotics. This review also summarizes key mechanisms in the biological treatment of antibiotics and evaluates risks associated with major ARB/ARG removal processes. Our aim is to enhance understanding of ARB risks, their pathways and mechanisms in biotreatment, and potential biomedical applications for pollution control.},
}

@article {pmid41011422,
year = {2025},
author = {Elbir, H},
title = {Genomic and Phylogenomic Characterization of Three Novel Corynebacterium Species from Camels: Insights into Resistome, Mobilome Virulence, and Biochemical Traits.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092090},
pmid = {41011422},
issn = {2076-2607},
abstract = {The genus Corynebacterium is commonly isolated from camel uteri, yet it is rarely identified to the species level. During our routine clinical examination of she-camels brought to the hospital with history of reproductive and systemic health issues, four isolates from the uterus and one isolate from blood could not be assigned to any valid Corynebacterium species. Therefore, we aim to identify these isolates, determine any potential virulence factors, and describe how gene turnover contributed to the evolution of these species. Genome-based and phenotypic identification, along with resistome, mobilome, virulome and phylogenomics analysis, was used to characterize the isolates. The isolates were Gram stain-positive, catalase-positive, and rod-shaped. The isolates were assigned to the genus Corynebacterium based on 16S rRNA gene sequence similarity and phylogenetic analysis. The isolates 3274 and ayman were classified as two new Corynebacterium species based on the average nucleotide identity (ANI) values of 78.46% and 68.88% and digital DNA-DNA hybridization (dDDH) values of 20.9% and 22.4%. The isolates 2581A, 2583C, and 4168A constitute a single Corynebacterium species based on their pairwise ANI value of 99% and dDDH value of more than 90%. In addition, isolates 2581A, 2583C, and 4168A showed ANI values of 75.99%, 75.86%, and 76.04% and dDDH values of 23.1%, 23%, and 22.5% with closely related species, and were designated as single new Corynebacterium species. Genes for mycolic acid and menaquinone biosynthesis were detected in all isolates. The isolates were susceptible to ceftiofur, linezolid, penicillin, erythromycin, and tetracycline. All isolates harbored the antiseptic resistance gene qacA. Moreover, virulence factors involved in cell adhesion and iron acquisition were detected. The evolution of these species is dominated by gene gain rather than gene loss. The majority of these genes are acquired through horizontal gene transfer, mediated by prophages and genomic islands. In summary, we characterized three new Corynebacterium species, expanding the number of new Corynebacterium species from animals. Moreover, we described the mechanism underlying the genome evolution of these new species. The clinical findings and detection of virulence genes highlight the significance of these isolates as possible pathogens, contributing to the development of endometritis in camels.},
}

@article {pmid41011419,
year = {2025},
author = {Ma, J and Xu, L and Shang, K and He, QY and Zhang, G},
title = {RecA Inhibitor Mitigates Bacterial Antibiotic Resistance.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092087},
pmid = {41011419},
issn = {2076-2607},
support = {2023YFA0915800//Ministry of Science and Technology of China, National Key Research and Development Program/ ; },
abstract = {Bacterial antibiotic resistance (AR) has become a critical global health threat. AR is mainly driven by adaptive resistance mutations and the horizontal gene transfer of resistance genes, both of which are enhanced by genome recombination. We previously discovered that genome recombination-mediated tRNA upregulation is important for AR, especially in the early stages. RecA is a crucial bacterial factor mediating genome recombination and the DNA damage response. Therefore, RecA inhibitors should be effective in reducing AR. In this study, we found that BRITE-338733 (BR), a RecA inhibitor, can prevent ciprofloxacin (CIP) resistance in subculturing Escherichia coli strain BW25113 in the early stages (up to the 7th generation). In the presence of BR, the tRNA was decreased, so the bacteria cannot evolve resistance via the tRNA upregulation-mediated AR mechanism. The RecA expression level was also not increased when treated with BR. Transcriptome sequencing revealed that BR could inhibit oxidative phosphorylation, the electron transport chain process, and translation, thereby reducing the bacterial energy state and protein synthesis. Also, the effective concentrations of BR do not harm human cell viability, indicating its clinical safety. These findings demonstrate that BR effectively delays the emergence of spontaneous AR by targeting RecA-mediated pathways. Our findings shed light on a new strategy to counteract clinical AR: applying BR with the antibiotics together at the beginning.},
}

@article {pmid41011399,
year = {2025},
author = {Kim, S and Jeong, H and Lee, NK and Kang, DK and Paik, HD and Park, YS and Lee, JH},
title = {Comprehensive Safety Assessment of Lentilactobacillus buchneri KU200793 as a Potential Probiotic.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092067},
pmid = {41011399},
issn = {2076-2607},
support = {GCU-202406430001//Gachon University/ ; 321035052HD020//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry/ ; },
abstract = {The safety profile of Lentilactobacillus buchneri KU200793, which has neuroprotective effects, was comprehensively evaluated through both phenotypic and genotypic analyses. Phenotypically, the strain exhibited no β-hemolysis, mucin degradation, indole production, gelatin liquefaction, urease activity, or β-glucuronidase activity. Additionally, it did not produce D-lactate, and only trace amounts of spermidine were detected among the biogenic amines. Furthermore, L. buchneri KU200793 did not exhibit bile salt deconjugation, further supporting its safety profile. However, its tetracycline resistance exceeded the threshold set by the European Food Safety Authority. Genotypic analysis using the HGTree program identified tetA(58) and nalD genes with sequence similarities of 33.64% and 30.17%, respectively, indicating a low level of homology. These findings suggest that tetracycline resistance in L. buchneri KU200793 is unlikely to have been acquired through horizontal gene transfer, thereby minimizing the risk of resistance gene dissemination. This study underscores the importance of comprehensive safety assessments to evaluate the suitability of L. buchneri KU200793 for probiotic applications.},
}

@article {pmid41009907,
year = {2025},
author = {Iorgoni, V and Stanga, L and Iancu, I and Degi, J and Popa, I and Gligor, A and Orghici, G and Sicoe, B and Dreghiciu, IC and Purec, D and Nistor, P and Florea, B and Kracunović, C and Herman, V},
title = {Multidrug-Resistant Escherichia coli Associated with Respiratory and Systemic Infection in a Domestic Rabbit in Romania: First Confirmed Case.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090929},
pmid = {41009907},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: This report documents the first confirmed case in Romania of fatal pneumonia and septicemia in a domestic rabbit caused by multidrug-resistant Escherichia coli, highlighting both its pathogenic potential and One Health implications.

CASE STUDY: An 8-month-old male German Giant Spotted rabbit raised on a rural farm under poor husbandry conditions developed acute respiratory distress and died within 48 h. Post-mortem examination revealed severe pulmonary congestion, tracheal inflammation, serofibrinous pericarditis, and systemic vascular lesions. Bacteriological analysis confirmed E. coli from lung, trachea, and bone marrow samples. The isolate demonstrated strong Congo red binding, was confirmed by MALDI-TOF mass spectrometry, and showed resistance to beta-lactams, fluoroquinolones, tetracyclines, sulfonamides, macrolides, and phenicols, remaining susceptible only to aminoglycosides. PCR screening identified virulence genes (fimH, papC, iutA, ompA) linked to adhesion, immune evasion, and iron acquisition, with potential for horizontal gene transfer.

CONCLUSIONS: This first documented case in Romania emphasizes the clinical threat posed by multidrug-resistant E. coli in rabbits and the importance of early diagnosis, improved biosecurity, and responsible antimicrobial use. The zoonotic and environmental risks in backyard farming underscore the urgent need for integrated surveillance. Alternative control strategies, including phage therapy and probiotics, should be explored to reduce reliance on conventional antibiotics.},
}

@article {pmid41009900,
year = {2025},
author = {Ngan, WY and Rao, S and Fung, AHY and Habimana, O},
title = {Genomic Profiling Reveals Clinically Relevant Antimicrobial Resistance and Virulence Genes in Klebsiella pneumoniae from Hong Kong Wet Markets.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090922},
pmid = {41009900},
issn = {2079-6382},
support = {104006142.095798.26000.301.01//The University of Hong Kong's University Research Committee Seed Fund for Basic Research/ ; GCII-Seed-202409//GTIIT-Changzhou Innovation Institute/ ; },
abstract = {Background:Klebsiella pneumoniae is a highly dangerous microorganism that presents significant challenges to effectively eliminate in food production facilities, making it a serious and urgent public health concern. The wet markets of Hong Kong represent a considerable yet insufficiently explored source for the spread of microorganisms. Methods: This investigation employed whole-genome sequencing and comparative genomics to assess the genomic variation and adaptive traits of K. pneumoniae extracted from wooden cutting boards in these marketplaces. We examined four wet market isolates in conjunction with 39 publicly accessible genomes from diverse origins. Results: Pan-genome analysis revealed a diverse and open genetic structure significantly shaped by horizontal gene transfer. Phylogenetic reconstruction did not categorize the wet market isolates into a singular clade, indicating varied contamination sources; nonetheless, certain market isolates exhibited close phylogenetic affiliations with high-risk clinical clones, implying possible spillover events. These isolates exhibited a concerning variety of antimicrobial resistance genes (ARGs), chiefly encoding efflux pumps (acrAB, oqxAB), which confer resistance to numerous drug categories. Moreover, the evaluation for pathogenicity attributes uncovered genes associated with robust biofilm development (fim and mrk operons) and efficient iron procurement strategies. Conclusions: The existence of these genetically adaptable isolates, possessing multidrug resistance and virulence factors, renders wet markets potential amplifiers and reservoirs for the spread of resistant pathogens. These findings present the initial genomic evidence of such risks in Hong Kong's wet markets and emphasize the immediate necessity for improved hygiene protocols and comprehensive One Health surveillance to reduce transmission at the human-animal-environment interface.},
}

@article {pmid41009471,
year = {2025},
author = {Miftode, IL and Vâţă, A and Miftode, RŞ and Oancea, AF and Pasăre, MA and Parângă, TG and Miftode, EG and Mititiuc, IL and Radu, VD},
title = {The Gut Microbiome and Colistin Resistance: A Hidden Driver of Antimicrobial Failure.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
doi = {10.3390/ijms26188899},
pmid = {41009471},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Colistin/pharmacology/therapeutic use ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Colistin, a polymyxin antibiotic reintroduced as a last-resort therapy against multidrug-resistant Gram-negative bacteria, is increasingly being compromised by the emergence of plasmid-mediated colistin resistance genes (mcr-1 to mcr-10). The human gut microbiota serves as a major reservoir and transmission hub for these resistance determinants, even among individuals without prior colistin exposure. This review explores the mechanisms, dissemination, and clinical implications of mcr-mediated colistin resistance within the gut microbiota, highlighting its role in horizontal gene transfer, colonization, and environmental persistence. A comprehensive synthesis of the recent literature was conducted, focusing on epidemiological studies, molecular mechanisms, neonatal implications and decolonization strategies. The intestinal tract supports the enrichment and exchange of mcr genes among commensal and pathogenic bacteria, especially under antibiotic pressure. Colistin use in agriculture has amplified gut colonization with resistant strains in both animals and humans. Surveillance gaps remain, particularly in neonatal populations, where colonization may occur early and persist silently. Promising interventions, such as fecal microbiota transplantation and phage therapies, are under investigation but lack large-scale clinical validation. The gut microbiome plays a central role in the global spread of colistin resistance. Mitigating this threat requires integrated One Health responses, improved diagnostics for gut colonization, and investment in microbiome-based therapies. A proactive, multisectoral approach is essential to safeguard colistin efficacy and address the expanding threat of mcr-mediated resistance.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Colistin/pharmacology/therapeutic use
*Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid41004892,
year = {2025},
author = {Okada, K and Wongboot, W and Roobthaisong, A and Hanchanachai, N and Doung-Ngern, P and Okada, PA and Wongchai, T and Swaddiwudhipong, W and Iida, T and Hamada, S},
title = {Genomic analyses of enteroinvasive Escherichia coli revealed the circulation of conjugative virulence plasmids and emergence of novel clones.},
journal = {International journal of medical microbiology : IJMM},
volume = {321},
number = {},
pages = {151677},
doi = {10.1016/j.ijmm.2025.151677},
pmid = {41004892},
issn = {1618-0607},
abstract = {Enteroinvasive Escherichia coli (EIEC) is a diarrhoeagenic E. coli pathotype that shares key virulence traits with Shigella, including the invasion plasmid (pINV). In Thailand, an outbreak caused by the EIEC serotype O8:H19-the first reported in the country-occurred in 2023, affecting over 150 patients. To elucidate the emergence, clinical relevance, and epidemiological distribution of EIEC in Thailand, we conducted a comprehensive investigation. We isolated and genomically characterised 63 isolates, comprising 28 EIEC (eight serotypes, including O96:H19 from a 2024 outbreak) and 35 Shigella (25 S. sonnei and 10 S. flexneri), along with 85 global reference strains. Comparative genomics revealed that the 2023 and 2024 EIEC outbreak isolates, along with a novel OX18:H25 EIEC lineage, harboured highly similar pINV plasmids with conserved invasion genes and complete conjugation elements. These isolates retained several biochemical traits that were more typical of commensal E. coli than classical EIEC. Limited chromosomal genome reduction-a hallmark of Shigella- was observed, which suggests that these lineages are in an early stage of adaptation toward a pathogenic lifestyle. Phylogenomic analysis showed that OX18:H25 is closely related to livestock-associated E. coli, supporting the hypothesis that pINV was recently acquired via horizontal gene transfer. These findings highlight the active circulation of putatively conjugative virulence plasmids among E. coli populations and the ongoing emergence of novel EIEC clones with epidemic-inducing potential.},
}

@article {pmid41003748,
year = {2025},
author = {Sundar Rajan, M and Jayavelu, T and Pennathur, G},
title = {Phylogenetic Studies on Taurine Dioxygenase (TauD).},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {526},
pmid = {41003748},
issn = {1432-0991},
support = {DBT/2017/Anna Univ/966//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Phylogeny ; Promoter Regions, Genetic ; Gene Transfer, Horizontal ; *Bacteria/enzymology/genetics/classification ; Taurine/metabolism ; Operon ; *Mixed Function Oxygenases/genetics/metabolism ; Fungi/genetics/enzymology ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Taurine dioxygenase (TauD) catalyses α-ketoglutarate-dependent oxidative decomposition of taurine and is grouped into an eponymous protein family (Pfam 02668-Taurine Catabolism Dioxygenase TauD, TfdA) with other enzymes that share this domain, but differ in substrates. In this study, we have detected Low Complexity Regions (LCRs) that set TauD apart from other members of its family. Using these regions, we designed patterns that reliably give true hits when queried against UniProt. We further demonstrate the use of these LCRs in detecting horizontal gene transfer (HGT) that led to TauD incorporation in at least one fungus genome. Additionally, we studied the genomic context of tauD across bacterial species and also performed promoter analysis to gain insights into its regulation. The tauABCD operon is restricted to certain genera of class Gammaproteobacteria with few exceptions, suggesting inheritance from a common ancestor. In other classes, TauD was found to have diverse genomic neighbours. Promoter analysis reveals several global and local regulators for tauABCD operon and other operons containing tauD.},
}

*Phylogeny
Promoter Regions, Genetic
Gene Transfer, Horizontal
*Bacteria/enzymology/genetics/classification
Taurine/metabolism
Operon
*Mixed Function Oxygenases/genetics/metabolism
Fungi/genetics/enzymology
Bacterial Proteins/genetics/metabolism

@article {pmid41003510,
year = {2025},
author = {Ding, Q and Liu, T and Li, Z and Sun, R and Zhang, J and Yin, L and Pu, Y},
title = {Comprehensive Insight into Microcystin-Degrading Mechanism of Sphingopyxis sp. m6 Based on Mlr Enzymes.},
journal = {Toxins},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/toxins17090446},
pmid = {41003510},
issn = {2072-6651},
support = {2024M760442//China Postdoctoral Science Foundation funded project/ ; GZC20240246//Postdoctoral Fellowship Program of CPSF/ ; 82404225, 81972997//the National Nature Science Foundation of China/ ; },
mesh = {*Microcystins/metabolism ; *Sphingomonadaceae/genetics/enzymology/metabolism ; *Bacterial Proteins/metabolism/genetics ; Biodegradation, Environmental ; },
abstract = {Bacterial degradation is one important Microcystin (MC) removal method in the natural environment. The traditional MC-degrading pathway was proposed based on the functions of individual recombinant Mlr enzymes and the structures of the main MC-degrading products. However, the actual MC-degrading mechanism by Mlr enzymes in wild-type bacteria remains unclear. In this study, bioinformatic analysis, heterologous expression, and knockout mutation were performed to elaborate the MC-degrading mechanism by Mlr enzymes in Sphingopyxis sp. m6. The results showed that mlr gene cluster was initially acquired by horizontal gene transfer, followed by vertical inheritance within Alphaproteobacteria. Mlr enzymes exhibit distinct subcellular localizations and possess diverse conserved catalytic domains. The enzymatic cascade MlrA/MlrB/MlrC sequentially cleaves Microcystin-LR (MC-LR) via Adda-Arg, Ala-Leu, and Adda-Glu bonds, generating characteristic intermediates (linearized MC-LR, tetrapeptide, and Adda). Notably, recombinant MlrC demonstrated dual-targeting degrading capability (linearized MC-LR and tetrapeptide), while tetrapeptide specificity in endogenous processing of Sphingopyxis sp. m6. Marker-free knockout mutants of mlr genes were first constructed in MC-degrading bacteria, unveiling that mlrA was indispensable in initial MC cleavage, whereas mlrB/mlrC/mlrD displayed functional compensation through other enzymes with similar functions. This study promotes the mechanistic understanding of MC bacterial degradation and offers a theoretical basis for a bioremediation strategy targeting cyanotoxin pollution.},
}

*Microcystins/metabolism
*Sphingomonadaceae/genetics/enzymology/metabolism
*Bacterial Proteins/metabolism/genetics
Biodegradation, Environmental

@article {pmid41003187,
year = {2025},
author = {Chattopadhyay, P and Banerjee, G},
title = {Diversity and Distribution of Non-Reducing Polyketide Synthases (NR-PKSs) in Ascomycota (Fungi).},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090641},
pmid = {41003187},
issn = {2309-608X},
abstract = {(1) Background: This study highlights the diversity and distribution of non-reducing polyketide synthases (NR-PKSs) in Ascomycota and their role in producing bioactive aromatic polyketides. (2) Methods: A reference dataset of non-NR-PKSs was compiled from published literature and cross-examined using NaPDoS2 and Kyoto Encyclopedia of Genes and Genomes Ortholog (KEGG KO) databases. Signature domains were validated through Pfam and CDD, while phylogenetic classification was conducted by comparing the dataset with the NaPDoS2 reference tree. Cluster support was derived from KEGG KO and homology-based modeling. Additionally, NR-PKS clade distribution across KEGG genomes was analyzed, and co-expression patterns were examined using STRING. (3) Results: This study identified nine distinct clades of NR-PKSs, six of which are supported by unique KEGG Orthology (KO) numbers. These clades are as follows: clade 1: polyketide synthase A (PksA, K15316); clade 2: fusarubinsynthase 1 (Fsr1); clade 3: white A (WA, K15321); clade 4: polyketide synthase citrinin (PksCT); clade 5: zearalenone synthase 1 (Zea1, K15417); clade 6: orsellinic acid synthase A (OrsA, K15416); clade 7: aurofusarin polyketide synthase A (AptA, K15317); clade 8: monodictyphenone polyketide synthase G (MdpG, K15415); and clade 9: bikaverin polyketide synthase (Bik1). The present investigation also reports incongruency in the distribution of different NR-PKSs and fungi phylogeny within the phylum Ascomycota. (4) Conclusions: The distribution of NR-PKSs in Ascomycota defies phylogenetic boundaries, reflecting the impact of horizontal gene transfer, gene loss, and ecological adaptation.},
}

@article {pmid41002241,
year = {2025},
author = {Kurushima, J and Nomura, T and Ota, N and Tomita, H},
title = {Complete genomes of clade A1 and B Enterococcus faecium isolates harboring pHTβ, a vanA-type vancomycin-resistant pMG1-like plasmid.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0068425},
doi = {10.1128/mra.00684-25},
pmid = {41002241},
issn = {2576-098X},
abstract = {Enterococcal conjugative plasmids play a key role in the widespread expansion of antimicrobial resistance genes among Enterococcus faecium via horizontal gene transfer. Herein, we report the complete genomes of clinical E. faecium isolates harboring pHTβ, a pMG1-like plasmid containing an inserted vancomycin resistance operon.},
}

@article {pmid41001059,
year = {2025},
author = {Thoenen, L and Hummerjohann, J and Schwendimann, L and Marti, E},
title = {Phenotypic and genotypic characterization of antibiotic-resistant bacteria from Swiss ready-to-eat meat products.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649307},
pmid = {41001059},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global health concern, which is partly driven by rising meat consumption, which has led to the intensive farming of livestock that relies on antibiotics. ready-to-eat animal products can carry antibiotic-resistant bacteria, posing risks to humans since they are often consumed without further cooking. While countries such as Switzerland limit antibiotic use in agriculture, contamination of meat with antibiotic-resistant bacteria can still occur during meat processing, and non-antibiotic agents such as heavy metals may contribute to the co-selection of resistance. This study aimed to characterize antibiotic-resistant bacteria in ready-to-eat meat products from various Swiss butcheries. Presumptive resistant bacteria were isolated using selective plating and analyzed phenotypically and genotypically. A total of 53 bacteria-antibiotic resistance combinations were identified, including Enterobacterales resistant to third-generation cephalosporins, vancomycin-resistant Enterococci, and one strain of methicillin-resistant Staphylococcus aureus. Of the 804 products sampled, 177 antibiotic-resistant bacteria were isolated, 148 of which showed multidrug resistance. Notably, these strains remained susceptible to last-resort antibiotics such as carbapenems and colistin. Whole-genome sequencing of 31 selected isolates revealed 164 antibiotic resistance genes spanning 25 classes, confirming resistance to beta-lactams, cephalosporins, and tetracyclines. We also detected genes conferring resistance to metals, suggesting co-selection pressures. Long-read sequencing revealed that the majority of the antibiotic resistance genes were chromosomal, while others were plasmid-encoded, indicating the potential for horizontal gene transfer. This study demonstrates that ready-to-eat meat products are reservoirs of antibiotic and metal resistance genes, as well as antibiotic-resistant bacteria, even at low levels. From a One Health perspective, our results highlight the importance of extending AMR surveillance across the food chain and underscore the need to include non-traditional bacterial indicators.},
}

@article {pmid41000824,
year = {2025},
author = {Ejikeugwu, CP and Edeh, C and Nwakaeze, EA and Adikwu, MU and Torres, C and Creevey, CJ and Eze, PM},
title = {Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.18.677015},
pmid = {41000824},
issn = {2692-8205},
abstract = {BACKGROUND: Broad and unregulated antibiotic use in livestock production, particularly poultry farming, has increased the development and persistence of multidrug-resistant (MDR) bacterial strains in animals. These resistant pathogens and their antibiotic resistance genes (ARGs) can spread to humans through environmental exposure and the food chain, posing serious public health risks. Whole-genome sequencing (WGS), alongside phenotypic antimicrobial susceptibility testing (AST), enables a comprehensive understanding of resistance mechanisms and informs antimicrobial stewardship strategies, particularly in resource-limited settings.

AIM: This study aimed to characterize the phenotypic and genotypic antimicrobial resistance profiles, plasmid content, and virulence factors of an MDR E. coli strain (S3) isolated from a poultry farm in Enugu State, Nigeria, to elucidate potential risks to public health and the role of poultry as a reservoir for resistance determinants.

METHODS: E. coli strain S3 was isolated from chicken droppings using standard microbiological methods and confirmed by MALDI-TOF mass spectrometry. AST was assessed using disc diffusion and broth microdilution to determine minimum inhibitory concentrations (MICs) for ten antibiotics across multiple classes. WGS was performed with a hybrid approach combining Illumina and Nanopore platforms, followed by genome assembly and annotation. ARGs, plasmid replicons, and virulence factors were identified in silico using AMRFinderPlus, starAMR, RGI/CARD, PlasmidFinder, MOB-suite, and the Virulence Factor Database (VFDB).

RESULTS: Phenotypic testing revealed extensive resistance, with complete resistance to six of seven tested antibiotics (cefotaxime, ampicillin, erythromycin, gentamicin, ciprofloxacin, and doxycycline). MICs exceeded clinical breakpoints for multiple classes, confirming an MDR phenotype. Genome analysis indicated a 5.33 Mb genome distributed across five contigs, including one chromosome and four plasmid-associated contigs. The strain harboured numerous ARGs, including [bla] CTX-M-15 , [bla] OXA-1 , [bla] TEM-1, aac(6')-Ib-cr, aadA5, aph(3'')-Ib, sul1/sul2, tet(A), dfrA17 , and mph(A) , co-localized on plasmids indicative of horizontal gene transfer (HGT) potential. Plasmid types included Col156, IncF, and two rep clusters. Virulence profiling revealed genes associated with adhesion (pap cluster, ECP), iron acquisition (enterobactin, yersiniabactin, aerobactin, heme uptake), and toxins (sat, senB), highlighting the isolate's potential for urinary tract and intestinal infections.

CONCLUSION: This study highlights the significant role of poultry-associated bacteria as reservoirs of AMR genes, particularly those harboured on mobile plasmids with potential for HGT. E. coli strain S3 exhibits extensive multidrug resistance and carries a complex plasmid repertoire facilitating horizontal transfer of ARGs. Coupled with a rich virulence gene profile, this strain underscores the public health risk posed by poultry-associated E. coli in Nigeria. These findings demonstrate the urgent need for stringent antimicrobial stewardship, regulatory oversight, and genomic surveillance in poultry production milieus to mitigate the dissemination of MDR pathogens.},
}

@article {pmid41000675,
year = {2025},
author = {Komine, T and Sathianpitayakul, P and Sakagami, N and Yoshida, M and Suzuki, M and Hoshino, Y and Ratthawongjirakul, P and Ato, M and Fukano, H},
title = {Plasmid-mediated macrolide resistance among rapidly growing mycobacteria in Japan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.17.676775},
pmid = {41000675},
issn = {2692-8205},
abstract = {OBJECTIVES: The spread of a transmissible plasmid carrying the 23S rRNA methylase gene erm (55), which confers inducible macrolide resistance in rapidly growing mycobacteria (RGM), has raised significant clinical concerns. The aim of this study was to investigate the prevalence of erm (55)-carrying plasmids in clinically isolated RGM strains in Japan.

METHODS: In total, 607 RGM clinical isolates, representing 32 species or complexes, collected between 2019 and 2023 in Japan were examined. To detect the presence of erm (55)-carrying plasmids, we conducted PCR screening, minimum inhibitory concentration testing for clarithromycin, and whole-plasmid genome sequencing. Comparative genomic analyses were performed to characterise the plasmids.

RESULTS: Among the 607 RGM isolates, 0.8% (5/607) possessed the plasmid with the erm (55) gene and exhibited inducible macrolide resistance, with ratios of 100% (1/1) in Mycobacterium murale , 50% (3/6) in M. obuense , and 0.8% (1/125) in M. chelonae . The erm (55)-carrying plasmids ranged from 126,187 to 170,220 bp in size. Pairwise BLASTn comparisons of the erm (55)-carrying plasmids showed weighted percent identity values ranging from 99.5% to 99.9%, with query and subject coverage values ranging from 74.2% to 100%. All erm (55) sequences (813 bp) were identical and located within a horizontal gene transfer region.

CONCLUSIONS: This study confirmed the presence of macrolide-resistant RGMs related to the erm (55)-carrying plasmid in Japan, although the overall prevalence remains low. These findings emphasise the need to consider plasmid-mediated resistance when treating infections caused by the RGM species.},
}

@article {pmid40999775,
year = {2025},
author = {Sabio, L and Day, GJ and Salmeron-Sanchez, M},
title = {Probiotic-Based Materials as Living Therapeutics.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e08500},
doi = {10.1002/adma.202508500},
pmid = {40999775},
issn = {1521-4095},
support = {Devise 101054728/ERC_/European Research Council/International ; EP/X033554/1//EPSRC HT2050/ ; EP/Y03029X/1//UK Research and Innovation (UKRI)/ ; 10052844//UK government's Horizon Europe/ ; 101070913//European Union under Horizon Europe project PRISM-LT/ ; },
abstract = {The growing demand for safer, more targeted therapeutics requires the development of advanced biomaterials. Among these, Engineered Living Materials (ELMs)-which integrate synthetic biology with material science-are emerging as promising platforms for biomedical applications. This review focuses on a subclass of ELMs based on genetically engineered probiotics combined with matrices, that are termed Probiotic Living Materials (PLMs) to differentiate them from Living Biotherapeutic Products (LBPs). Recent studies highlight PLM's potential in addressing different health conditions, offering targeted and dynamic therapies. However, PLMs face multiple challenges to be implemented in clinics, including a lack of robust genetic toolkits for probiotic engineering, concerns about biosafety (e.g., horizontal gene transfer or non-desirable biological activity), difficulties in translating preclinical results to humans, and the absence of clear regulatory guidance for clinical use. This review first explores the fundamental features of ELMs, then provides an overview of probiotics, followed by recent advances in the design of engineered PLMs for biomedical applications, particularly in biosensing development, infection treatment, bone repair, wound healing, vaginal imbalances, gut-related conditions, and cancer therapy. Finally, biosafety issues and current gaps in regulatory frameworks to ensure safe and effective use of PLMs, with a particular focus on vulnerable populations, are discussed.},
}

@article {pmid40997705,
year = {2025},
author = {Sheng, B and Liu, S and Xiong, K and Liu, J and Zhu, S and Zhang, H and Zhang, R},
title = {Response of bacterial pathogens to process upgrades and floc sizes in a full-scale landfill leachate treatment plant.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127377},
doi = {10.1016/j.jenvman.2025.127377},
pmid = {40997705},
issn = {1095-8630},
abstract = {Bacterial pathogens in wastewater environments pose serious public health risks, serving as reservoirs for antibiotic resistance genes (ARGs) and contributing to the global antimicrobial resistance (AMR) crisis. This study investigated how process upgrades and sludge aggregate sizes influence the distribution of bacterial pathogens and ARGs in a full-scale landfill leachate treatment plant (LLTP). Using 16S rRNA and metagenomic sequencing, we analyzed potential pathogens and ARG profiles during the progression from conventional nitrification-denitrification (CND) to partial nitrification-denitrification (PND). Results showed a notable increase in the relative abundance of potential pathogenic genera in large aggregates following the process upgrade, indicating structural and functional shifts in microbial communities. The average abundance of WHO-priority ARGs, including baeR, smeR, and adeL, was significantly higher at the PND phase, likely linked to the process upgrade. Additionally, the activity of mobile genetic elements (MGEs), particularly those involved in horizontal gene transfer and DNA repair, was enhanced at the PND phase, accelerating ARG dissemination. Importantly, the process upgrade reduced the relative abundance of Streptococcus pyogenes, a high-risk pathogen, suggesting improved pathogen control. This study provides critical insights into optimizing LLTP processes to mitigate AMR risks and improve public health safety.},
}

@article {pmid40997562,
year = {2025},
author = {Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Chen, Y and Wang, L and Wang, X and Jia, R and Wu, F and Li, Y},
title = {Metagenomic profiling of antibiotic resistance genes in terrestrial ecosystems across China.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119096},
doi = {10.1016/j.ecoenv.2025.119096},
pmid = {40997562},
issn = {1090-2414},
abstract = {Soil represents a significant reservoir of antibiotic resistance genes (ARGs), yet their distribution across diverse terrestrial ecosystems remains poorly characterized. To address this knowledge gap, we conducted a large-scale, cross-regional soil survey spanning 4300 km in China, collecting samples at 42 intervals across six distinct terrestrial ecosystems. High diversity (18 ARG types and 129 ARG subtypes) and abundance (mean value: 724.9 [coverage, ×/Gb]) of ARGs were observed in the topsoil (0-20 cm depth) across the six terrestrial ecosystems, with tetracycline resistance and efflux pump being the prevailing class and resistance mechanism respectively. Notably, only aac (6')-I ranked among the highest-risk ARGs (Rank I), indicating that merely 0.78 % of detected ARGs pose a severe pathogenic threat. Meanwhile, horizontal gene transfer (HGT) is likely the primary transmission mechanism for ARGs in these soils. While most ARGs currently present minimal direct public health risks, their high transmission potential warrants attention. Furthermore, stochastic processes dominate the spread of soil ARGs, though both stochastic and deterministic processes contribute to the spread of their hosts. Collectively, these results provide timely insights into the resistance mode of soil ARGs in terrestrial ecosystems.},
}

@article {pmid40988758,
year = {2025},
author = {Azad, RB and Kasfy, SH and Molla, K and Islam, T},
title = {Horizontal Gene Transfer in Plants and Implications for Biotechnology.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {5},
pages = {e70087},
pmid = {40988758},
issn = {2575-6265},
abstract = {Horizontal gene transfer (HGT), a fundamental process long acknowledged in prokaryotic evolution, is increasingly recognized as a pivotal force in shaping the evolutionary trajectories of eukaryotes, including plants. Despite its established significance in prokaryotic adaptation, the role of HGT in eukaryotic evolution is still understudied. HGT plays a pivotal role in the evolution of eukaryotes, giving rise to novel features that allow organisms to exploit new environments and resources with reduced competition. Moreover, the coevolution of interacting organisms in any ecosystem is greatly influenced by HGT. Recent discoveries of HGT events among eukaryotic species such as gene transfers from fungi to plants and from plants to whiteflies highlight the importance of understanding this phenomenon in the context of plant biology. In this review, we provide an update of recent findings related to plant and associated organisms like microorganisms, insects, and critically discuss the profound implications of HGT for plant evolution and adaptation, probing into potential underlying mechanisms, highlighting the knowledge gap and discussing their implications. In particular, we explore the potential applications of the new knowledge of HGT in plant biotechnology, illuminating its pivotal role in shaping the future landscape of bioengineering.},
}

@article {pmid40986369,
year = {2025},
author = {Ratna, TA and Sharon, BM and Barros Velin, CA and Palmer, K},
title = {Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harboured by Enterococcus faecalis laboratory model strains and clinical isolates.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {9},
pages = {},
doi = {10.1099/mic.0.001601},
pmid = {40986369},
issn = {1465-2080},
mesh = {*Enterococcus faecalis/genetics/drug effects/isolation & purification ; *Plasmids/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Humans ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; Gram-Positive Bacterial Infections/microbiology ; },
abstract = {Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor, and laboratory model strains as donor versus recent human isolates as donor during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both WT and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared with 4-log for pCF10). Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defence, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens and highlighting pTEF2 as a plasmid for additional mechanistic study.},
}

*Enterococcus faecalis/genetics/drug effects/isolation & purification
*Plasmids/genetics
*CRISPR-Cas Systems/genetics
Gene Transfer, Horizontal
Conjugation, Genetic
Humans
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics
Gram-Positive Bacterial Infections/microbiology

@article {pmid40985733,
year = {2025},
author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM},
title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0057425},
doi = {10.1128/aem.00574-25},
pmid = {40985733},
issn = {1098-5336},
abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.

IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.},
}

@article {pmid40804527,
year = {2025},
author = {Gavrilov, AA and Shamovsky, I and Zhegalova, I and Proshkin, S and Shamovsky, Y and Evko, G and Epshtein, V and Rasouly, A and Blavatnik, A and Lahiri, S and Rothenberg, E and Razin, SV and Nudler, E},
title = {Elementary 3D organization of active and silenced E. coli genome.},
journal = {Nature},
volume = {645},
number = {8082},
pages = {1060-1070},
pmid = {40804527},
issn = {1476-4687},
mesh = {*Escherichia coli/genetics/cytology ; *Genome, Bacterial/genetics ; Escherichia coli Proteins/metabolism/genetics ; *Chromosomes, Bacterial/genetics/chemistry/metabolism ; DNA-Binding Proteins/metabolism/genetics ; *Gene Silencing ; Nucleic Acid Conformation ; DNA, Bacterial/chemistry/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Molecular Chaperones ; },
abstract = {Unravelling how genomes are spatially organized and how their three-dimensional (3D) architecture drives cellular functions remains a major challenge in biology[1,2]. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid[3-5]. Despite progress in characterizing bacterial 3D genome architecture over recent decades[6-8], the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods such as Hi-C[9-11]. Here we developed an enhanced Micro-C chromosome conformation capture, achieving 10-base pair (bp) resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the Escherichia coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, have key roles in repressing horizontally transferred genes. Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, whereas removing both H-NS and StpA results in their complete disassembly, increased transcription of horizontally transferred genes and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals that all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.},
}

*Escherichia coli/genetics/cytology
*Genome, Bacterial/genetics
Escherichia coli Proteins/metabolism/genetics
*Chromosomes, Bacterial/genetics/chemistry/metabolism
DNA-Binding Proteins/metabolism/genetics
*Gene Silencing
Nucleic Acid Conformation
DNA, Bacterial/chemistry/genetics/metabolism
Gene Transfer, Horizontal/genetics
Molecular Chaperones

@article {pmid40985701,
year = {2025},
author = {Boehlein, SK and Hennen-Bierwagen, TA and Shuler, SL and Tracy, WF and Hannah, LC and Resende, MFR and Myers, AM},
title = {Interactions of separately conserved α-(1→6) glucosidases that participate in maize endosperm starch biosynthesis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf417},
pmid = {40985701},
issn = {1532-2548},
abstract = {Chloroplast-containing species possess two α-(1→6)-glucosidases that share a common ancestor but were independently acquired by horizontal gene transfer from separate eubacterial donors. The pullulanase-type enzyme (CAZy subfamily GH13_13) and the isoamylase-type enzyme (CAZy subfamily GH13_11) both hydrolyze branch linkages in α-polyglucans. Thus, both enzyme types function as debranching enzymes (DBE) in starch metabolism. As both enzyme types are conserved, distinct selectable functions are expected. This study describes the functional interactions between maize (Zea mays L.) pullulanase1 (ZPU1) and the isoamylase-type enzyme complex comprising the paralogous proteins isoamylase1 (ISA1) and isoamylase2 (ISA2). Mutation of ISA1 or ISA2 caused reduced ZPU1 activity in developing endosperm extracts, and the addition of ISA1 to ZPU1-expressing yeast (Saccharomyces cerevisiae) cells caused increased ZPU1 activity. Specific amino acid substitutions in ISA1 resulted in altered ZPU1 mobility in SDS-PAGE. In vivo protein-protein interaction tests and co-immunoprecipitation revealed that ZPU1 and ISA1 interact in multi-subunit complexes. Maize lines harboring ISA1 mutations, exhibiting a classical low-starch, high-phytoglycogen-accumulation phenotype, were altered by recurrent selection so that kernel appearance reverted to near normal. Extragenic suppression indicated the requirement for ISA1/ISA2 activity had been bypassed. These results are consistent with a functional overlap between the GH13_11 and GH13_13 DBE types and raise the possibility that multiple GH13 proteins, namely ZPU1, ISA1 and ISA2, act together to physically coordinate their hydrolytic activities on precursor α-polyglucans.},
}

@article {pmid40983639,
year = {2025},
author = {Dirick, L and Liu, Y and Dong, S and Yu, J and Ouerdane, L and Storti, M and Alboresi, A and Curie, C and Goffinet, B},
title = {Multiple independent acquisitions of a metallophore-synthesis gene by plants through horizontal microbial gene transfer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8339},
pmid = {40983639},
issn = {2041-1723},
support = {DEB-1753811//National Science Foundation (NSF)/ ; ANR-19-CE20-0009//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE20-0009//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; 202005//Urban Management Bureau of Shenzhen Municipality/ ; 202203//Urban Management Bureau of Shenzhen Municipality/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Evolution, Molecular ; *Plants/genetics ; *Bryophyta/genetics ; Fungi/genetics ; },
abstract = {The evolution of land plants is marked by major innovations enhancing their vegetative and reproductive fitness. Despite their extensive adaptations to terrestrial habitats, plants rely on ecological interactions with microbes for various physiological processes. Beyond their role as critical partners in the conquest of, and diversification on land, fungi and bacteria also serve as sources of genetic tools. Analyses of the gene space of land plant model organisms suggest that such transfers are unique and ancient. However here, using genomic data spanning the diversity of mosses, we demonstrate that a metallophore-synthesis gene was acquired independently from distinct microbial donors by at least five plant lineages. Furthermore we find that the first NAS gene acquired by mosses was later replaced by another fungal copy, transferred to another major moss lineage. Such a complex history of acquisition of a gene may reflect a more general pattern of highly dynamic gene exchange across the tree of life.},
}

*Gene Transfer, Horizontal
Phylogeny
Evolution, Molecular
*Plants/genetics
*Bryophyta/genetics
Fungi/genetics

@article {pmid40982302,
year = {2025},
author = {Liu, Z and Ma, C and Teng, X and Yu, K and Li, J},
title = {Emergence of Pediatric Sepsis Caused by a Klebsiella pneumoniae Strain Coharboring blaNDM-1, blaOXA-1, and Mcr-9 in China.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1177/10766294251380517},
pmid = {40982302},
issn = {1931-8448},
abstract = {This study reports the discovery of a Klebsiella pneumoniae (KPN) strain carrying the blaNDM-1, blaOXA-1, and mcr-9 genes in China for the first time. This strain was isolated from the blood of a 2-year-old pediatric patient with acute lymphoblastic leukemia and sepsis. The strain exhibited high resistance to various antibiotics, including β-lactams, carbapenems, and ceftazidime-avibactam. Through whole-genome sequencing and comparative genomic analysis, we found that these resistance genes coexisted on the transferable IncHI2/IncHI2A-type plasmid pK708696_1, which showed high similarity to plasmid pK710429_2 from strain KPN710429 previously identified in our hospital, indicating their potential for rapid spread through horizontal gene transfer. We also performed conjugation experiments to verify the transferability of the plasmid. The results show that the resistance of this strain to traditional antibiotics significantly limited clinical treatment options, thereby posing a serious threat, especially for pediatric leukemia patients with compromised immune systems. This study provides important scientific evidence and new therapeutic approaches for combating carbapenem-resistant Klebsiella pneumoniae infections and highlights the urgency of developing new antibiotics and alternative therapies.},
}

@article {pmid40980877,
year = {2025},
author = {Eriksson, H and Schlegel, S and Koskiniemi, S},
title = {A delivered DNase toxin creates population heterogeneity through transient intoxication of siblings.},
journal = {mBio},
volume = {},
number = {},
pages = {e0208325},
doi = {10.1128/mbio.02083-25},
pmid = {40980877},
issn = {2150-7511},
abstract = {UNLABELLED: Population heterogeneity is important for multicellular behavior, as well as bet-hedging strategies. Recent findings suggest a role for bacterial toxin delivery in generating population heterogeneity, but the molecular mechanisms by which this occurs are not well understood. Here, we address if and how delivery of bacterial CdiA toxins generates heterogeneity in an isogenic population of Escherichia coli (E. coli) cells. Using a DNase toxin as a proxy, we find that E. coli populations able to deliver the toxin show a heterogeneous expression of the SOS-response gene sulA, whereas those incapable of kin-delivery remain homogeneous. Heterogeneity results from excessive delivery of toxin into some cells, which become intoxicated due to insufficient immunity. A low level of intoxication by this toxin is transiently reversible, and intoxicated cells can be rescued by the de novo synthesis of cognate immunity protein. The fraction of cells experiencing toxicity is increased by liberating the receptor responsible for toxin import from its tasks in outer-membrane biogenesis, suggesting that kin-intoxication is limited by receptor availability. Expression of sulA is regulated by both DNA damage and redox status. Interestingly, kin-delivery changes redox status, whereas intoxicated non-kin cells induce the SOS DNA damage response. The former results in changed expression of metabolic genes, whereas the latter induces prophage excision, which may promote horizontal gene transfer. In conclusion, we identify a molecular mechanism by which heterogeneity is generated through toxin delivery among kin, and some of the consequences of said heterogeneity.

IMPORTANCE: Population heterogeneity is important for multicellularity, as well as for bet-hedging strategies. A heterogeneous population allows cells with the same genotype to respond differently to environmental cues and stresses. For multicellularity, heterogeneity originates from coordinated signaling, whereas bet-hedging strategies can arise stochastically due to cell-to-cell variation in the concentration of signaling molecules. However, recent advances suggest a role for bacterial toxin delivery in the generation of population heterogeneity. How toxins mediate heterogeneity mechanistically is, however, unclear. Here, we show that kin cells transiently intoxicate each other with CdiA toxins, resulting in physiological changes. These changes are specific to the toxic activity, i.e., other toxins with different activities are likely to give rise to other responses. Thus, we find that the arsenal of toxins that bacteria harbor could affect their ability to participate in bet-hedging strategies, as well as in multicellular behavior.},
}

@article {pmid40980327,
year = {2025},
author = {Mosca Angelucci, D and Piergiacomo, F and Donati, E and Pagani, L and Minuti, E and Brusetti, L and Tomei, MC},
title = {Combined effects of ciprofloxacin and microplastics on alpine spring water microbiota: evidence from glacier-fed microcosm experiments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654589},
pmid = {40980327},
issn = {1664-302X},
abstract = {INTRODUCTION: Emerging contaminants such as microplastics (MPs) and antibiotics pose increasing environmental and public health risks due to their persistence and incomplete removal by wastewater treatment processes. MPs can act as vectors for antibiotics, facilitating their environmental spreading and supporting biofilm formation, which can enhance horizontal gene transfer and antibiotic resistance. This study investigates the combined effects of ciprofloxacin (CIP) and polyethylene terephthalate (PET) MPs on microbiota in alpine spring water (SW) sourced from a rock glacier.

METHODS: Four experimental scenarios (Control, CIP, PET, CIP + PET) were established to assess the sorption dynamics of CIP onto PET particles and the consequent microbial responses. A multidisciplinary analytical approach combining ultra-performance liquid chromatography, microscopy, quantitative PCR, and metabarcoding was applied.

RESULTS: CIP exhibited progressive sorption onto PET, accompanied by a time-dependent increase in biofilm formation, most pronounced in the CIP + PET condition. qPCR revealed elevated copy numbers of resistance genes qnrA and qnrB in CIP + PET, suggesting synergistic effects between antibiotics and MPs in promoting resistance. CIP was the dominant driver of microbial compositional shifts, favoring known CIP-degrading taxa. A shared core microbiome of 216 amplicon sequence variants was detected across all conditions, but specific taxa were differentially enriched under varying exposures. The combined CIP + PET test induced the strongest community shifts, while CIP alone shared fewer taxa with controls, indicating selective pressure for resistant microorganisms like Achromobacter. PET MPs also shaped distinct microbial assemblages, possibly by offering niches favoring biofilm-associated genera such as Luteolibacter. Biodiversity metrics showed highest richness and evenness in CIP-free conditions (Control and PET), while CIP significantly reduced alpha diversity, favoring resistant taxa, as confirmed by NMDS and lower Shannon and Simpson indices. Effects of MPs were still noticeable.

CONCLUSION: These findings demonstrate the disruptive effects of CIP on alpine freshwater microbial communities and highlight the additional, though more moderate, influence of MPs. The combined presence of MPs and antibiotics may exacerbate resistance spreading by enhancing persistence and providing favorable conditions for resistant biofilms. A mechanistic understanding of these interactions is essential for accurate risk assessment and the development of effective mitigation strategies in alpine and other vulnerable freshwater ecosystems.},
}

@article {pmid40980325,
year = {2025},
author = {Lu, Y and Wen, Z and Liu, X and Zhang, T and Liu, M and Zhang, L and Qiu, J and Wang, M},
title = {Research progress on bacterial outer membrane vesicles in antibiotic resistance and clinical anti-infective therapy.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670307},
pmid = {40980325},
issn = {1664-302X},
abstract = {In recent years, bacterial outer membrane vesicles (OMVs)-nanoscale, bilayered membrane structures secreted by Gram-negative bacteria-have attracted considerable attention for their involvement in antibiotic resistance and potential in clinical anti-infective strategies. OMVs encapsulate diverse biomolecules, including proteins, lipids, toxins, and nucleic acids, thereby serving as critical mediators of communication between bacteria and host cells. They contribute to horizontal gene transfer, signal transduction, and biofilm formation, ultimately enhancing bacterial adaptability and resistance. Clinically, OMVs are regarded as promising therapeutic platforms owing to their excellent biocompatibility and intrinsic immunogenicity, with ongoing investigations exploring their roles in vaccine development, targeted drug delivery, and immune modulation. This review highlights the participation of OMVs in resistance mechanisms across common pathogenic bacteria and discusses their emerging applications in infection control. By elucidating the biogenesis and functional mechanisms of OMVs, novel antibacterial strategies may be developed, offering new avenues to address the escalating global challenge of antibiotic resistance.},
}

@article {pmid40979677,
year = {2025},
author = {Phuadraksa, T and Choominthong, Y and Wichit, S and Yainoy, S},
title = {Emergence of Klebsiella pneumoniae ST14 co-harboring bla NDM-1, bla OXA-232 , mcr-1.1, and a novel IncI1 tet(X4) plasmid, with evidence of ColKP3 mobilization under antibiotic pressure.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100466},
pmid = {40979677},
issn = {2666-5174},
abstract = {Companion animals and environmental niches act as interconnected reservoirs of antimicrobial resistance (AMR) genes, facilitating their persistence and horizontal transfer across hosts and ecosystems. Pet-associated environments, within the One Health framework linking human, animal, and environmental health, remain an underrecognized source of AMR dissemination. Pet grooming facilities generate wastewater containing bacteria from animal skin, fecal matter, and contaminated surfaces, potentially acting as factors that facilitate environmental contamination and zoonotic transmission. Here, we describe the isolation and complete genomic characterization of an extensively drug-resistant Klebsiella pneumoniae strain from wastewater at a pet grooming facility in Bangkok, Thailand. Whole-genome sequencing identified the isolate as sequence type (ST) 14, a globally disseminated high-risk clone associated with multidrug resistance and clinical outbreaks. The strain harbored four clinically significant resistance genes, bla NDM-1, bla OXA-232, mcr-1.1, and tet(X4), each located on distinct plasmids. To our knowledge, this is the first report of tet(X4) in K. pneumoniae ST14. The gene was found on a novel IncI1-type plasmid with a composite transposon, suggesting recent acquisition through horizontal gene transfer. Conjugation assays confirmed high transfer efficiency and phenotypic tigecycline resistance. In this study, although bla OXA-232 was carried on a non-conjugative ColKP3-type plasmid, colistin selection facilitated its transfer with plasmid size expansion, indicating antibiotic-driven mobilization. These findings highlight the evolutionary adaptability of K. pneumoniae ST14 and the risk posed by pet-associated wastewater as a reservoir for clinically important AMR genes. Integrated genomic surveillance and targeted One Health interventions are urgently needed to prevent environmental and zoonotic spread.},
}

@article {pmid40974529,
year = {2025},
author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z},
title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40974529},
issn = {1869-1889},
abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.},
}

@article {pmid40527433,
year = {2025},
author = {Zhu, C and Han, Y and Lu, Z and Yao, H},
title = {Impacts of particle size and surface charge of ZnO on horizontal transformation of antibiotic resistance genes.},
journal = {NanoImpact},
volume = {39},
number = {},
pages = {100571},
doi = {10.1016/j.impact.2025.100571},
pmid = {40527433},
issn = {2452-0748},
mesh = {*Zinc Oxide/chemistry/pharmacology ; *Escherichia coli/genetics/drug effects ; Particle Size ; Surface Properties ; Plasmids/genetics ; *Gene Transfer, Horizontal/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Nanoparticles/chemistry ; *Transformation, Bacterial/drug effects ; },
abstract = {The ever-growing antibiotic resistance in bacteria poses an enormous threat to public health and the environment. The horizontal transfer of antibiotic resistance genes (ARGs) is a major pathway for disseminating antibiotic resistance. As an inexpensive, nontoxic, and biocompatible material, ZnO with diverse sizes and surface properties have been prepared for widespread use. However, the effects and mechanisms of ZnO particles with different structural properties on the horizontal transfer of ARGs are not comprehensively understood. In this study, two groups of ZnO particles, one with the same size (93 nm) and different charge types (-9.5 and + 17.4 mV), and the other homogeneously positively charged but of different sizes (93, 215, and 2381 nm), were prepared. Their impacts on the horizontal transformation of ARGs mediated by plasmid pUC19 into E coli DH5α were investigated. In the positively charged group, the smallest ZnO nanoparticles at concentrations of 0.1-100 μg/mL induced 1.04-1.35 and 1.37-1.71-fold increases in transformation frequency when compared with that of the medium-sized and largest particles, respectively. In the similar-sized groups, positive ZnO promoted 1.06-1.32-fold increases than negative ZnO. Further investigation suggested that smaller and positive ZnO adsorbed more plasmids and correspondingly increased the uptake by recipient bacteria than that of larger and/or negative ZnO. In addition, the enhanced bacterial membrane permeability, ATP synthesis, and DNA replication were also accounted for the increased transformation. These results suggest that smaller-sized and positive ZnO poses a high environmental risk of spreading antibiotic resistance.},
}

*Zinc Oxide/chemistry/pharmacology
*Escherichia coli/genetics/drug effects
Particle Size
Surface Properties
Plasmids/genetics
*Gene Transfer, Horizontal/drug effects
Anti-Bacterial Agents/pharmacology/chemistry
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Nanoparticles/chemistry
*Transformation, Bacterial/drug effects

@article {pmid40973782,
year = {2025},
author = {Morimoto, D and Usutani, R and Tateishi, N and Funaoka, Y and Takahashi, M and Nagasaki, K},
title = {Co-infection of phylogenetically distinct nucleocytoviruses in Acanthamoeba castellanii cells.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf087},
pmid = {40973782},
issn = {1574-6968},
abstract = {Nucleocytoviruses have extraordinarily large double-stranded DNA genome, including a set of highly conserved genes for viral reproduction. Meanwhile, nucleocytoviruses supposedly acquire new genes from cellular organisms and different lineages of nucleocytovirus, leading to their evolution. Although horizontal gene transfer among nucleocytoviruses is thought to occur in the cell simultaneously infected by distinct nucleocytoviruses, it remains unknown which combination of lineages can co-infect host cell. Here, we performed co-infection experiments using cedratvirus, megavirus, mollivirus, and pandoravirus. By transmission electron microscopy, we observed Acanthamoeba castellanii cells incorporating two distinct viral species in all six combinations. Furthermore, A. castellanii cell incorporating all four viral species was observed. In these experiments, a simultaneous increase in viral particles was observed for the combination of mollivirus and pandoravirus, pandoravirus and cedratvirus, mollivirus and cedratvirus, and megavirus and cedratvirus. Furthermore, transcription levels of cedratvirus and megavirus genes in the co-infected culture were significantly lower than those in the mono-infected culture based on time-course experiments, suggesting that distinct nucleocytoviruses may compete for viral reproduction. This is the first report experimentally demonstrating that co-infection of distinct nucleocytoviruses occurs in A. castellanii cell.},
}

@article {pmid40972972,
year = {2025},
author = {Marcy, E and Chiek, S and Hidé, M and Hak, S and Ma, C and Lem, M and Delvallez, G and Bañuls, AL and Cheng, S and Hayer, J},
title = {Hybrid Sequencing of Chromosome and Plasmids from Multidrug Resistant Escherichia coli Isolated in Cambodia: Are Megaplasmids Vectors of Antibiotic Resistance Genes?.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.003},
pmid = {40972972},
issn = {2213-7173},
abstract = {OBJECTIVES: The prevalence of Antimicrobial Resistance (AMR) in Escherichia coli infections in Cambodia is high and increasing, yet data distinguishing plasmid- and chromosome-mediated AMR-spread remain limited. The aim of this study was to characterise chromosomal and plasmid structures in clinically relevant E. coli resistant strains to investigate mechanisms driving the spread of Antibiotic Resistance Genes (ARGs) in Battambang Province, Cambodia.

METHODS: Hybrid genome assembly was performed using short- and long-read sequencing of six Extended Spectrum Betalactamase (ESBL)- and Carbapenemase Producing (CP) E. coli isolates collected from patients at Battambang Provincial Hospital, Cambodia. Detailed bacteriological analyses were conducted, as well as comprehensive genomic investigations to characterise Sequence Types (STs), plasmids, resistance mechanisms, and phylogenetic relationships among the strains, and to perform pairwise comparisons of plasmid sequences.

RESULTS: Chromosome and plasmid sequences were successfully recovered for each strain. Five STs were identified: ST1193 (two strains), ST131, ST205, ST405 and ST4204. All strains displayed a megaplasmid carrying ARGs, and one to five regular-sized plasmids without ARGs. Four distinct megasplasmids sequences were identified, including one shared by two ST1193 strains and one shared by ST131 and ST205 strains.

CONCLUSIONS: The identification of megaplasmids carrying ARGs and shared by different strains highlights their potential role in the spread of antimicrobial resistance through horizontal gene transfer (HGT) in Cambodia. This study also confirms the circulation of the high-risk multidrug-resistant (MDR) clones ST131 and ST1193 in Battambang province, Cambodia, and underscores the importance of hybrid genome assembly to study plasmid structure and identify their role in AMR spread.},
}

@article {pmid40972703,
year = {2025},
author = {Bao, Y and Liu, G and Yao, H},
title = {Microplastic aging mediates bacterial and antibiotic resistance gene composition in plastisphere and the associated soil solution.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127134},
doi = {10.1016/j.envpol.2025.127134},
pmid = {40972703},
issn = {1873-6424},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are emerging contaminants that have garnered significant attention due to their prevalence in soil. Although many studies have already highlighted the effects of MPs on soil microbial communities and ARGs spread, their differential variation in both habitats (plastisphere and surrounding soil solution) and the effect of aging degree of MPs has not been clarified. Herein, we conducted a microcosm experiment to investigate the effects of aged-treated MPs on microbiome and antibiotic resistome of the plastisphere and the surrounding soil solution. The results showed that MPs with different aging degree altered bacterial community compositions. The plastisphere was enriched more unique bacterial species compared to its surrounding solution, particularly for 7d-aged MPs. MPs aging promoted certain ARGs dissemination, which depends on habitats, ARGs types and their aging degree. MPs always promoted the enrichment of Proteobacteria as the top host, especially aged MPs, which explained the enhanced ARGs dissemination after aged MPs addition. The primary hosts of most ARGs shifted from surrounding soil solution to the plastisphere. In addition to these individual host species, population hosts, including key taxa within co-occurrence network modules and functional bacterial populations, also contributed to ARGs dissemination. Unique bacteria from the plastisphere were included in network key modules and promoted ARGs dissemination, but not in the solution. Bacterial functions and pathways both played pivotal roles in ARGs dissemination. Interestingly, the influence of these population-level hosts, along with associated bacterial functions and metabolic pathways, on ARG spread was more pronounced in the surrounding soil solution than in the plastisphere. According to variance partitioning analysis, horizontal gene transfer via MGEs plays an important role in ARGs dissemination with 54-78% contribution in two habitats. Overall, these findings provide the differential processes and driving mechanisms of ARGs dissemination between the plastisphere and surrounding soil solution.},
}

@article {pmid40971805,
year = {2025},
author = {Neupane, DP and Bearson, BL and Bearson, SMD},
title = {Localization of the origin of transfer (oriT) for Salmonella Genomic Island 4 (SGI-4) from Salmonella enterica serovar I 4, [5],12:i:.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf023},
pmid = {40971805},
issn = {1756-1663},
abstract = {Salmonella enterica serovar I 4, [5],12:i:- (serovar I 4, [5],12:i:-) is one of the most frequent multidrug-resistant (MDR) Salmonella serovars associated with food-animal production globally, and strains often contain Salmonella genomic island-4 (SGI-4), an integrative conjugative element (ICE) encoding metal tolerance for copper, silver, and arsenic. Horizontal gene transfer (HGT) of SGI-4 from serovar I 4, [5],12:i:- to recipient bacteria results in enhanced metal tolerance for the transconjugants; however, the origin of transfer (oriT) for SGI-4 mobilization is unknown. In this study, the oriT within SGI-4 of MDR serovar I 4, [5],12:i:- strain USDA15WA-1 was identified by: a) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and b) deleting the predicted oriT region of SGI-4 from strain USDA15WA-1 and abolishing SGI-4 transfer. Sequence similarity to oriTSGI-4 was identified in other Enterobacteriaceae, and conjugation of SGI-4 occurred from USDA15WA-1 to Salmonella serovars from serogroups C-E as well as Escherichia coli and Citrobacter. Localization of the SGI-4 oriT enhances our understanding of a DNA region involved in HGT of an ICE in a frequent MDR Salmonella serovar, thereby providing a model to investigate HGT of SGI-4 and dissemination of metal tolerance genes in the food-animal production environment.},
}

@article {pmid40971384,
year = {2025},
author = {Cuesta-Morrondo, S and Garita-Cambronero, J and Cubero, J},
title = {Unraveling the genomic complexity of secretion systems in the most virulent Xanthomonas arboricola pathovars.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332834},
doi = {10.1371/journal.pone.0332834},
pmid = {40971384},
issn = {1932-6203},
mesh = {*Xanthomonas/genetics/pathogenicity ; *Bacterial Secretion Systems/genetics ; *Genome, Bacterial ; Virulence/genetics ; Plant Diseases/microbiology ; Bacterial Proteins/genetics/metabolism ; Genomics ; Phylogeny ; },
abstract = {Xanthomonas arboricola pathovars pruni (Xap), juglandis (Xaj), and corylina (Xac) are phytopathogenic bacteria that infect Prunus spp., walnut, and hazelnut trees, respectively. In this study, the understanding of the differences among these pathovars was improved with the aim of elucidating their host range and uncovering distinct virulence mechanisms. A comparative genomic analysis was conducted focusing on secretion system clusters across high-quality genomes from two strains of each pathovar. The results revealed that the RaxABC type I secretion system was absent in all analyzed strains. However, the HlyDB type I secretion system was present in both Xap and Xac, with a putative HlyDB effector identified in each Xac strain. Additionally, Xap strains contained a putative PctAB type I secretion system, while only one of the Xac harbored a putative PctAB. Notably, the genomic region surrounding pctA and pctB lacked pctP, suggesting the presence of a novel type I secretion system rather than the canonical PctAB. In contrast, Xaj lacked all the studied type I secretion systems. While the core components of type II and type III secretion systems were highly conserved across strains, significant variation was observed in their substrates. Interestingly, only Xap carried two pathovar-specific type III effectors. Regarding type V secretion systems, complete homologs of EstA, YapH, and XadA were found in all strains, except for one Xac strain, which contained a frameshifted YapH. Additionally, homologs of the XacFhaB/XacFhaC system were found in both Xap strains. However, both Xaj strains and one Xac strain carried an incomplete XacFhaB subunit, while the other Xac strain lacked this system entirely. Finally, analysis of the genomic regions surrounding these secretion system clusters strongly suggests that horizontal gene transfer has played a crucial role in their acquisition, likely contributing to the diversification, emergence and specialization of distinct X. arboricola pathovars.},
}

*Xanthomonas/genetics/pathogenicity
*Bacterial Secretion Systems/genetics
*Genome, Bacterial
Virulence/genetics
Plant Diseases/microbiology
Bacterial Proteins/genetics/metabolism
Genomics
Phylogeny

@article {pmid40970135,
year = {2025},
author = {Gutiérrez-Escobar, AJ and Srinivasan, M and Muñoz-Ramirez, ZY and Vale, FF and Wang, D and Sandoval-Motta, S and Dekker, JP and Thorell, K and Camargo, MC and Yamaoka, Y and Fischer, W},
title = {Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.25.671524},
pmid = {40970135},
issn = {2692-8205},
abstract = {Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori , a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICE Hptfs3 and ICE Hptfs4 , and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (Hp GP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.},
}

@article {pmid40796352,
year = {2025},
author = {Namias, A and Martinez, J and Boussou, I and Terretaz, K and Conner, WR and Justy, F and Makoundou, P and Perriat-Sanguinet, M and Labbé, P and Sicard, M and Landmann, F and Weill, M},
title = {Recombination, Truncation and Horizontal Transfer Shape the Diversity of Wolbachia-induced Cytoplasmic Incompatibility Patterns.},
journal = {Molecular biology and evolution},
volume = {42},
number = {9},
pages = {},
doi = {10.1093/molbev/msaf200},
pmid = {40796352},
issn = {1537-1719},
support = {R35GM124701//US National Institutes of Health/ ; //MUSE/ ; },
mesh = {*Wolbachia/genetics ; Animals ; *Gene Transfer, Horizontal ; Male ; Female ; *Culex/microbiology/genetics ; Recombination, Genetic ; Cytoplasm ; Polymorphism, Genetic ; Symbiosis ; },
abstract = {Wolbachia are endosymbiotic bacteria inducing various reproductive manipulations of which cytoplasmic incompatibility is the most common. Cytoplasmic incompatibility leads to reduced embryo viability in crosses between males carrying Wolbachia and uninfected females or those carrying an incompatible symbiont strain. In the mosquito Culex pipiens, the Wolbachia wPip causes highly complex crossing patterns. This complexity is linked to the amplification and diversification of the cytoplasmic incompatibility causal genes, cidA and cidB, with polymorphism located in the CidA-CidB interaction regions. We previously showed that some compatibility patterns correlated with the presence or absence of specific cid variants. It is still unknown, however, whether cid gene polymorphism alone is sufficient to explain the diversity of crossing patterns observed in Cx. pipiens. Taking advantage of a new method enabling full-gene acquisition, we sequenced complete cid repertoires from 45 wPip strains collected worldwide. We demonstrated that the extensive diversity of cid genes arises from recombination and horizontal transfers. We uncovered further cidB polymorphism located outside the interface regions and strongly correlated with cytoplasmic incompatibility patterns. Most importantly, we showed that in every wPip genome, all but one cidB variant are truncated. Truncated cidBs located in palindromes are partially or completely deprived of their deubiquitinase domain, crucial for cytoplasmic incompatibility. The identity of the sole full-length cidB variant seems to dictate cytoplasmic incompatibility patterns, irrespective of the truncated cidBs present. Truncated CidBs exhibit reduced toxicity and stability in Drosophila cells, which potentially hinders their loading into sperm, essential for cytoplasmic incompatibility induction.},
}

*Wolbachia/genetics
Animals
*Gene Transfer, Horizontal
Male
Female
*Culex/microbiology/genetics
Recombination, Genetic
Cytoplasm
Polymorphism, Genetic
Symbiosis

@article {pmid40970083,
year = {2025},
author = {Hoshino, N and Kuroda, H},
title = {Possible Horizontal Gene Transfer of Novel Transposable Elements in Anisakis simplex between Hosts and Parasites.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
doi = {10.17912/micropub.biology.001578},
pmid = {40970083},
issn = {2578-9430},
abstract = {Tc1 / mariner transposons found in salmoniform fish have been identified in both closely and distantly related fish species, suggesting that horizontal gene transfer may have occurred. However, the vectors of this process remain unknown. We identified two homologous sequences in the parasitic nematode Anisakis simplex , naming them Tas1 (T ransposable element of A nisakis s implex number 1) and Tas2 . These elements encode Tc1 / mariner transposases structurally similar to the active Sleeping Beauty transposase. Furthermore, Tas1 / 2 were also identified in organisms that serve as hosts for Anisakis . These findings suggest that Tas1 / 2 may have undergone horizontal gene transfer within host-parasite interactions.},
}

@article {pmid40966505,
year = {2025},
author = {Couturier, A and Fraikin, N and Lesterlin, C},
title = {Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes.},
journal = {Nucleic acids research},
volume = {53},
number = {17},
pages = {},
doi = {10.1093/nar/gkaf898},
pmid = {40966505},
issn = {1362-4962},
support = {FRM-EQU202103012587//Foundation for Medical Research/ ; ANR-22-CE12-0032//French National Research Agency/ ; ANR-23-CE12-0037//French National Research Agency/ ; },
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Homeostasis/genetics ; *Escherichia coli/genetics ; SOS Response, Genetics ; *Drug Resistance, Bacterial/genetics ; Genetic Fitness ; Gene Transfer, Horizontal ; },
abstract = {Plasmid conjugation is a major driver of antibiotic resistance dissemination in bacteria. In addition to genes required for transfer and maintenance, conjugative plasmids encode exclusion systems that prevent host cells from acquiring identical or redundant plasmids. Despite their ubiquity, the biological impact of these systems remains poorly understood. Here, we investigate the importance of the exclusion mechanism for plasmid dynamics and bacterial physiology at the single-cell level. Using real-time microscopy, we directly visualize how the absence of exclusion results in plasmid unregulated self-transfer, causing continuous and repeated plasmid exchange among host cells. This runaway conjugation severely compromises cell integrity, viability, and fitness, a largely undescribed phenomenon termed lethal zygosis. We demonstrate that lethal zygosis is associated with membrane stress, activation of the SOS response, and potential reactivation of SOS-inducible prophages, as well as chromosome replication and segregation defects. This study highlights how exclusion systems maintain host cell homeostasis by limiting plasmid transfer. Paradoxically, this restriction is critical to the successful dissemination of conjugative plasmids by conferring a selective advantage, which explains their evolutionary conservation and underscores their role in the spread of antibiotic resistance among pathogenic bacteria.},
}

*Plasmids/genetics
*Conjugation, Genetic
Homeostasis/genetics
*Escherichia coli/genetics
SOS Response, Genetics
*Drug Resistance, Bacterial/genetics
Genetic Fitness
Gene Transfer, Horizontal

@article {pmid40962902,
year = {2025},
author = {Sivabalasarma, S and Taib, N and Mollat, CL and Joest, M and Steimle, S and Gribaldo, S and Albers, SV},
title = {Structure of a functional archaellum in Bacteria of the Chloroflexota phylum.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40962902},
issn = {2058-5276},
support = {403222702-SFB 1381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403222702-SFB 1381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403222702-SFB 1381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403222702-SFB 1381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 506518771//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ENVOL//Fondation Bettencourt Schueller (Bettencourt Schueller Foundation)/ ; },
abstract = {Motility in Archaea is driven by the archaellum, a rotary ATP-driven machinery unrelated to the bacterial flagellum. To date, archaella have been described exclusively in archaea; however, recent work reported archaellum genes in bacterial strains of the SAR202 clade (Chloroflexota). Here, using MacSyFinder, we show that bona fide archaellum gene clusters are widespread in several members of the Chloroflexota. Analysis of archaellum-encoding loci and Alphafold3-predicted structures show similarity to the archaellum machinery. Using cryo electron microscopy single-particle analysis, we solved the structure of the bacterial archaellum from Litorilinea aerophila to 2.7 Å. We also show the expression and assembly of this machinery in bacteria and its function in swimming motility. Finally, a phylogenomic analysis revealed two horizontal gene transfer events from euryarchaeal members to Chloroflexota. In summary, our study shows that a functional and assembled archaellum machinery can be exchanged between the two prokaryotic domains.},
}

@article {pmid40961345,
year = {2025},
author = {Colombi, E and Ghaly, TM and Rajabal, V and Elbourne, LDH and Gillings, M and Tetu, S},
title = {Adaptative and ancient co-evolution of integrons with Xanthomonas genomes.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001503},
pmid = {40961345},
issn = {2057-5858},
mesh = {*Integrons/genetics ; *Xanthomonas/genetics/classification ; Phylogeny ; *Evolution, Molecular ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Integrases/genetics ; },
abstract = {Integrons are genetic elements that facilitate gene acquisition. They have been extensively studied in clinical bacteria, but their evolutionary role in phytopathogens remains underexplored. Here, we analysed complete genomes of Xanthomonas species to investigate the origin, distribution and functional dynamics of integrons in this genus. We found that 93% of genomes harboured integrons. The integron-integrase gene intI was predominantly located downstream of ilvD, indicating an ancestral acquisition of integrons, predating diversification within the genus. Phylogenetic analyses support vertical inheritance of intI, with the exception of rare horizontal gene transfer events, notably in Xanthomonas arboricola. Despite their widespread presence, full-length intI genes and active integron platforms are only retained in some species, especially Xanthomonas campestris, which shows high integron gene cassette variability and functional integron activity. In contrast, species such as Xanthomonas cissicola and Xanthomonas phaseoli exhibit widespread intI inactivation, likely occurring early in their divergence, leading to more stable cassette arrays and conserved integron-associated phenotypes. The number and diversity of genes within cassette arrays varied significantly by species and, to a lesser extent, by the ecological context of plant host cultivation. While most cassettes encoded proteins without a known function, those with annotated roles were associated with stress response mechanism, competitive exclusion and plant-associated functions. Together, our findings demonstrate that integrons in Xanthomonas likely originated from a single ancient acquisition event, preceding genus-wide speciation, and have co-evolved with Xanthomonas pathovars as they adapted to distinct plant hosts.},
}

*Integrons/genetics
*Xanthomonas/genetics/classification
Phylogeny
*Evolution, Molecular
*Genome, Bacterial
Gene Transfer, Horizontal
Integrases/genetics

@article {pmid40961326,
year = {2025},
author = {Nghiem, MN and Bui, DP and Ha, VTT and Tran, HT and Nguyen, DT and Vo, TTB},
title = {Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001500},
pmid = {40961326},
issn = {2057-5858},
mesh = {*Acinetobacter baumannii/genetics/isolation & purification/drug effects/classification/pathogenicity ; Vietnam ; Humans ; *Acinetobacter Infections/microbiology/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Phylogeny ; Whole Genome Sequencing ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Genetic Variation ; Polymorphism, Single Nucleotide ; Microbial Sensitivity Tests ; Plasmids/genetics ; Genomic Islands ; },
abstract = {Multidrug-resistant Acinetobacter baumannii poses a significant threat to hospital environments worldwide, including Vietnam. In this study, we conducted whole-genome sequencing on 30 clinical A. baumannii isolates from Hanoi to explore their genomic diversity, antibiotic resistance determinants, virulence factors and mobile genetic elements. Phylogenetic analyses, utilizing both SNP-based and multilocus sequence typing-based approaches, revealed that the isolates clustered into various sequence types (STs). Among these, ST2 and ST571 emerged as the dominant high-risk clones. The ST2 isolates exhibited a wide range of resistance genes, such as bla OXA-23, mph(E), msr(E) and armA. Additionally, they contained mobile genetic elements, including plasmids and AbaR-type resistance islands, which promote horizontal gene transfer. Virulence gene analysis showed the presence of several key determinants like ompA, adeFGH and bfmRS and quorum sensing regulators abaI and abaR, underscoring the strains' potential for persistent colonization and infection. These findings highlight the marked genomic diversity and robust resistance profiles of Vietnamese A. baumannii isolates. The predominance of ST2 and ST571, corresponding to global clones GC2 and GC1, respectively, along with frequent co-occurrence of bla OXA-23 and armA, suggests region-specific features distinct from those reported in other parts of Southeast Asia. This underscores the need for improved surveillance and targeted infection control strategies.},
}

*Acinetobacter baumannii/genetics/isolation & purification/drug effects/classification/pathogenicity
Vietnam
Humans
*Acinetobacter Infections/microbiology/epidemiology
*Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing
Phylogeny
Whole Genome Sequencing
Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Genetic Variation
Polymorphism, Single Nucleotide
Microbial Sensitivity Tests
Plasmids/genetics
Genomic Islands

@article {pmid40957209,
year = {2025},
author = {Feng, Y and Jiang, C and Zhang, W and Gong, L and Sun, L},
title = {Single and mixture toxicity effects of legacy and emerging per- and polyfluoroalkyl substances on submerged plants and epiphytic biofilms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139862},
doi = {10.1016/j.jhazmat.2025.139862},
pmid = {40957209},
issn = {1873-3336},
abstract = {Although per- and polyfluoroalkyl substances (PFASs), often referred to as "forever chemicals," pose persistent threats to aquatic ecosystems, the effects of multiple PFAS types on submerged macrophyte-biofilm symbiotic systems remain poorly understood. In this study, we systematically investigated the impacts of single and combined exposures to both legacy and emerging PFAS on submerged macrophytes, biofilms, and associated microbial risks. Our results show that the growth of Vallisneria natans was inhibited under both single and mixed PFAS stress. Photosynthetic performance and nutrient uptake in V. natans were variably affected depending on the PFAS type. Emerging PFAS were more likely to induce oxidative stress, with malondialdehyde content increasing by 36.7 % under hexafluoropropylene oxide dimer acid exposure. Notably, PFAS stress significantly altered biofilm morphology and microbial community composition, including enrichment of several human bacterial pathogens. Additionally, PFAS exposure promoted the enrichment of antibiotic resistance genes (ARGs), and the increased abundance of mobile genetic elements suggested a higher potential for horizontal gene transfer. Co-occurrence network analysis further revealed that potential ARG hosts were affected under PFAS stress.},
}

@article {pmid40957078,
year = {2025},
author = {Hernandez-Aranda, VA and Jarquin-Galvez, R and Aguilar-Benitez, G and Vega-Manriquez, DX and Vallejo-Pérez, MR and Escoto-Rodriguez, M and Winkler, R and Lara-Avila, JP},
title = {In silico analysis of secreted proteins via Sec- and Tat-pathways of Clavibacter spp. unravels functional diversity related to plant host range.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2025-0037},
pmid = {40957078},
issn = {1480-3321},
abstract = {Clavibacter genus comprises phytopathogenic and non-phytopathogenic species in a range of plant hosts. We applied structural and functional approaches for comparative genomics to unveil the adaptation of Clavibacter to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that C. tessallarius, C. zhangzhiyongii, C. capcisi, C. phaseoli depicted the more divergent species. Notably, C. nebraskensis, C. insidiosus, C. sepedonicus, Clavibacter sp. A6099, C. californiensis, and C. michiganensis formed a recent monophyletic clade. A synteny degree and genome rearrangements were noted. The functional approach based on prediction-annotation of secreted proteins via Sec and Tat pathways, and the prediction of metabolite biosynthetic potential. Regarding to Sec- and Tat-secreted proteins, we focused on carbohydrate-active enzymes (CAZymes) and expansins. The repertoire of secreted CAZymes exhibited variation related to taxonomy of Clavibacter. The predicted expansins harbored domain variability, related to horizontal gene transfer. A heterogeneous distribution-conservation of biosynthetic genetic clusters (BGCs) regarding Clavibacter phylogeny was observed. Our results suggested that farm practices of plant hosts likely influence the evolutive history of Clavibacter spp. Furthermore, Sec-, Tat-mediated secreted proteins and metabolite diversity may underpin plant-Clavibacter interactions. Biological knowledge drives sustainable strategies aimed to control plant diseases caused by Clavibacter spp.},
}

@article {pmid40956426,
year = {2025},
author = {Roy, MK and Bhattacharjee, A and Singh, AK},
title = {Bacterial type IV secretion systems and spread of antimicrobial resistance: a study of potential inhibitors to T4SS-based resistance spread.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {263},
pmid = {40956426},
issn = {1432-072X},
support = {OLP-2403 and OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; },
mesh = {*Type IV Secretion Systems/metabolism/genetics/antagonists & inhibitors ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria/drug effects/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Humans ; *Bacteria/drug effects/genetics/metabolism ; },
abstract = {Antimicrobial resistance (AMR) is a major global health threat, mainly driven by the rapid spread of resistance genes through horizontal gene transfer (HGT). The Type IV Secretion System (T4SS) acts as a crucial molecular machinery that facilitates this process, allowing bacteria to transfer DNA, effector proteins, and virulence factors. This review systematically explores the structural and functional diversity of T4SS, its role in spreading AMR, and current methods for its inhibition. T4SS consists of a multi-protein complex that spans bacterial membranes, mediating conjugative plasmid transfer, host-pathogen interactions, and bacterial competition. Key components include ATPases, pilus structures, and membrane-associated proteins that show both conserved features and species-specific adaptations. These traits enable functional specialization across Gram-positive and Gram-negative bacteria, significantly contributing to the spread of vital resistance genes like extended-spectrum β-lactamases and carbapenemases via mobile genetic elements. Several approaches have been developed to inhibit T4SS and combat AMR. Small molecules targeting ATPase activity or protein interactions are promising, as are natural phytochemicals that interfere with conjugation. Bacteriophage therapy provides another strategy by specifically targeting plasmid-carrying bacteria. Host immune responses, such as innate immune recognition and secretory immunoglobulins, also show potential to influence T4SS activity. Although progress has been made, challenges remain, especially in developing selective inhibition methods that do not harm beneficial microbiota or host cells. Future research should focus on high-resolution structural studies to support rational drug design and preclinical testing of combination therapies that include T4SS inhibitors with existing antibiotics. Gaining a deeper understanding of T4SS regulation and host-pathogen interactions will be vital for creating targeted AMR strategies that also maintain ecological balance.},
}

*Type IV Secretion Systems/metabolism/genetics/antagonists & inhibitors
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
*Gram-Negative Bacteria/drug effects/genetics/metabolism
Bacterial Proteins/metabolism/genetics
Humans
*Bacteria/drug effects/genetics/metabolism

@article {pmid40956103,
year = {2025},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics.},
journal = {mBio},
volume = {},
number = {},
pages = {e0240925},
doi = {10.1128/mbio.02409-25},
pmid = {40956103},
issn = {2150-7511},
abstract = {UNLABELLED: Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus, as in clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immunity systems, and horizontal gene transfer (HGT), which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate concomitantly, but observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history trade-offs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable environments, direct interaction with the virus is the optimal route of immunity acquisition. In fluctuating, unpredictable environments with a moderate viral prevalence, horizontal transfer of defense genes is preferred. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete absence of defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes, such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles.

IMPORTANCE: The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via HGT, whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short-term evolution of prokaryotic immunity and showed that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy, whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.},
}

@article {pmid40956092,
year = {2025},
author = {Dossouvi, KM and Sambe Ba, B and Lo, G and Sellera, FP and Furlan, JPR and Culot, A and Abriat, G and Gueye, AB and Ba-Diallo, A and Dieng, A and Ly, FP and Cissé, A and Ndiaye, SML and Tine, A and Karam, F and Diagne-Samb, H and Ngom-Cisse, S and Diop-Ndiaye, H and Toure-Kane, C and Gaye-Diallo, A and Dossim, S and Mboup, S and Boye, CSB and Seck, A and Camara, M},
title = {Clinical carbapenem-resistant Enterobacterales in a University Hospital in Dakar, Senegal: genomic insights into Enterobacter hormaechei ST182 strains carrying blaNDM-5 and blaOXA-48 genes .},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0078025},
doi = {10.1128/spectrum.00780-25},
pmid = {40956092},
issn = {2165-0497},
abstract = {Senegal has witnessed the emergence and spread of carbapenem-resistant Enterobacterales (CRE), which often cause deadly infections. Accordingly, this study aimed to determine the antimicrobial susceptibility and prevalence of carbapenemases, as well as to perform a whole-genome sequence analysis of clinical CRE isolates from a university hospital in Dakar, Senegal. MALDI-TOF MS and VITEK2 systems were used for bacterial identification and antimicrobial susceptibility testing (AST). Carbapenemase- and cephalosporinase-encoding genes were screened using simplex end-point polymerase chain reaction. Whole-genome sequencing (WGS) was performed using the Illumina MiSeq platform. The CRE isolates were resistant to almost all the 34 antimicrobials tested. Nevertheless, colistin and amikacin remained active, with susceptibility rates of 96% and 71%, respectively. Only the carbapenemase genes blaOXA-48 (53.8%; 15/28) and blaNDM (35.7%; 10/28) and the cephalosporinase gene blaCMY-1 (25%; 7/28) were identified. In this context, two extensively drug-resistant Enterobacter hormaechei isolates were subjected to WGS analysis. These isolates were assigned as sequence type (ST) 182 and carried several genes related to antimicrobial resistance (AMR), metal tolerance, and virulence. An IncL/M plasmid with 61,054 bp in length was identified as carrying the blaOXA-48 gene, whereas an IncFIB(pECLA)/IncFII(pECLA)/IncX3 mutireplicon plasmid with 217,745 bp in length was detected as harboring the blaNDM-5 gene and other genes related to AMR and metal tolerance. Our study presents the first landscape of clinical CRE circulating in Senegal, along with additional genomic analysis of E. hormaechei ST182 strains, which could be useful for mitigating the burden associated with CRE in this country.IMPORTANCEThe investigation of global critical priority CRE isolates has become crucial to reduce morbidity and mortality associated with AMR. This study revealed that colistin and amikacin can be considered good alternatives for treating CRE-associated infections in Dakar. In addition, the genomic approach revealed that the CRE isolates carried both a wide resistome and virulome. Moreover, the abundance of horizontal gene transfer regions in the genomes suggests the great implications of mobile genetic elements in the spread of AMR in Dakar. Furthermore, this study reported the complete sequences of chromosomes and blaOXA-48 and blaNDM-5-carrying plasmids. Our findings are of great importance because complete genome sequences are still rarely characterized in the West African region. Finally, this study highlights the importance of strengthening genomic surveillance of CRE in sub-Saharan African countries to mitigate the burden associated with these pathogens.},
}

@article {pmid40954939,
year = {2025},
author = {Chen, J and Wang, M and Liu, H and Li, Z},
title = {Novel Substitutes of Phthalate Esters (PAEs) Promote the Propagation of Antibiotic Resistance Genes via Ferroptosis: Implication for the Environmental Safety Evaluation of PAE Substitutes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10489},
pmid = {40954939},
issn = {1520-5851},
abstract = {The horizontal transfer of antibiotic resistance genes (ARGs) has become a major threat to global public health. Recent studies have found that ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation and glutathione depletion, may play a critical role in the dissemination of ARGs among environmental microbes. Here, we demonstrated for the first time that phthalate esters (PAEs) and their substitutes significantly enhanced plasmid conjugation by triggering ferroptosis-related pathways. Classical ferroptosis-associated responses, including the hyperpolarization of the cell membrane potential, elevated production of reactive oxygen species, and heightened membrane permeability, were observed under the stress of PAEs or their substitutes. Through integrated transcriptomic and metabolomic analyses, we revealed that these compounds triggered iron dysregulation via the upregulation of iron acquisition and storage pathways while suppressing DNA replication, concurrently causing oxidative damage that stimulated the plasmid conjugation. Molecular docking simulations revealed that PAEs and their substitutes competitively disrupted the functionality of ferric uptake regulator (Fur) protein, a master controller of intracellular iron homeostasis, with superior binding affinity than its natural ligand Fe[2+]. Integrated metagenomic sequencing and homology analyses demonstrated the conservation of Fur protein across biofilm microbiota and functional implications in iron homeostasis. Structural analysis based on the characteristic molecular fingerprints of chemicals pinpointed aliphatic chains as the crucial structure responsible for enhancing ARG propagation between bacteria. Our findings uncovered a mechanism by which PAEs and their substitutes exacerbated ARG dissemination through ferroptosis-mediated conjugation, providing crucial insights for environmental risk assessment and resistance mitigation strategies.},
}

@article {pmid40953126,
year = {2025},
author = {Banerjee, S and Shende, SS and Kata, L and Lopes, RS and Praveen, S and Joshi, R and Khare, NK and Raghuram, GV and Shabrish, S and Mittra, I},
title = {Horizontally transferred cell-free chromatin particles function as autonomous 'satellite genomes' and vehicles for transposable elements within host cells.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40953126},
issn = {2050-084X},
support = {CTC-TMC//Department of Atomic Energy, Government of India/ ; },
mesh = {Animals ; Mice ; Humans ; *Chromatin/genetics/metabolism ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; NIH 3T3 Cells ; *DNA, Satellite/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Fibroblasts ; },
abstract = {Horizontal gene transfer (HGT) plays an important evolutionary role in prokaryotes, but it is less frequent in mammals. We previously reported that cell-free chromatin particles (cfChPs) - chromosomal fragments released from the billions of dying cells that circulate in human blood - are horizontally transferred to healthy cells with biological effects. However, the underlying mechanism and function of these effects remained unclear. We treated NIH3T3 mouse fibroblasts cells with cfChPs isolated from human serum and serially passaged the cells. The intracellular activities of cfChPs were analysed using chromatin fibre fluorography, cytogenetic analysis, immunofluorescence, and fluorescent in situ hybridisation. We discovered that the internalised cfChPs were almost exclusively comprised of non-coding DNA, and the disparate DNA sequences contained within them had randomly combined to form complex concatemers, some of which were multi-mega base pairs in size. The concatemers autonomously performed many functions attributable to the nuclear genome such as DNA, RNA and protein synthesis. They harboured human LINE-1 and Alu elements, with the potential to rearrange themselves within the mouse genome. Our results suggest that a cell simultaneously harbours two autonomous genome forms: one that is inherited (hereditary genome) and numerous others that are acquired (satellite genomes). The satellite genomes may have evolutionary functions given their ability to serve as vehicles for transposable elements and to generate a plethora of novel proteins. Our results also suggest that 'within-self' HGT may occur in mammals on a massive scale via the medium of cfChP concatemers that have undergone extensive and complex modifications resulting in their behaviour as 'foreign' genetic elements.},
}

Animals
Mice
Humans
*Chromatin/genetics/metabolism
*DNA Transposable Elements
*Gene Transfer, Horizontal
NIH 3T3 Cells
*DNA, Satellite/genetics/metabolism
In Situ Hybridization, Fluorescence
Fibroblasts

@article {pmid40774041,
year = {2025},
author = {Long, J and Wu, J and Xi, Y and Zhang, J and Chen, S and Yang, H and Duan, G},
title = {Association between Type IV-A CRISPR/Cas system and plasmid-mediated transmission of carbapenemase genes in Klebsiella pneumoniae.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128297},
doi = {10.1016/j.micres.2025.128297},
pmid = {40774041},
issn = {1618-0623},
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Klebsiella pneumoniae/genetics/enzymology/drug effects ; *CRISPR-Cas Systems/genetics ; Humans ; Klebsiella Infections/microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {The global rise of carbapenem-producing K. pneumoniae is largely attributed to plasmid-mediated transmission of carbapenemase genes. Type IV-A CRISPR/Cas system is mainly located on plasmids in K. pneumoniae and involved in plasmid competition. However, the role of Type IV-A system in the dissemination of carbapenemase genes in K. pneumoniae remains unclear. Here, we comprehensively investigated the relationship between Type IV-A system and plasmid-mediated transmission of carbapenemase genes based on 152 K. pneumoniae clinical strains and 46226 K. pneumoniae public genomes available in NCBI database. We found that the presence of Type IV-A system was positively associated with blaNDM-1, blaNDM-5, blaOXA-48, and blaVIM-1 but negatively related to blaKPC-2, blaKPC-3,blaIMP and blaOXA-181. Additionally, plasmids carrying Type IV-A system were predominantly the vehicles of blaNDM-1 gene. Protospacer search revealed that Type IV-A system frequently matched conjugation transfer region of blaKPC-2-related IncF plasmids, especially IncFIB(K)/IncFII(K), IncFII(pHN7A8)/IncR, and IncFIB(pQil)/IncFII(K) plasmids. The prevalence of self-targeting event further highlighted the interference mechanism of transcriptional repression proposed by Type IV system. Despite frequent targeting of IncF plasmids by Type IV-A system, different types of IncF plasmids displayed varying distribution between CRISPR-positive and -negative genomes, thereby suggesting a differentiated response of Type IV-A system to IncF plasmids. Our results underscore complex interactions between Type IV-A system and plasmid-mediated carbapenemase genes, revealing its significant role in shaping the transmission dynamics of carbapenemase-encoding plasmids.},
}

*beta-Lactamases/genetics
*Plasmids/genetics
*Bacterial Proteins/genetics
*Klebsiella pneumoniae/genetics/enzymology/drug effects
*CRISPR-Cas Systems/genetics
Humans
Klebsiella Infections/microbiology
*Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid40580511,
year = {2025},
author = {Ren, X and Xiao, B and Wu, M and Yang, K and Gu, P and Zhang, Z and Miao, H},
title = {Effect and mechanism of residual-chlorine on the horizontal transfer of antibiotic resistance genes of chlorine resistant bacteria in reclaimed water.},
journal = {Environmental technology},
volume = {46},
number = {23},
pages = {4667-4680},
doi = {10.1080/09593330.2025.2516055},
pmid = {40580511},
issn = {1479-487X},
mesh = {*Chlorine/pharmacology ; *Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Microbial/genetics ; Water Microbiology ; Disinfectants/pharmacology ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Microbial Sensitivity Tests ; },
abstract = {Chlorine disinfection inactivates most microbes in reclaimed water, but chlorine resistant bacteria (CRB) persist, threatening water safety and spreading antibiotic resistance genes (ARGs). ARG proliferation in reclaimed water systems risks public health, as dissemination via irrigation or urban reuse may enable environmental transmission to humans, exacerbating global antibiotic resistance. One hundred and fifty-two strains of CRB were isolated from reclaimed water in this study, and the detection rate of ARGs in those CRB was 100%, the detection rate for blTEM was 100%, followed by sul3 and tetG. Macrogenomic analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes are the dominant CRB in reclaimed water. Long-term induction with the minimum inhibitory concentration (MIC) of NaClO enhanced the resistance of CRB to both Amp and NaClO. The EPS of CRB increased 1.30- to 2.04-fold, and the elevated surface hydrophobicity may serve as a co-resistance mechanism. EPS hindered disinfectant/antibiotic penetration, while hydrophobicity reduced hydrophilic molecule adhesion and promoted bacterial aggregation, both of which contribute to the enhanced resistance of CRB. Residual chlorine dose-dependently enhances ARG conjugation via ROS-SOS, ATP, and EPS pathways, unveiling novel CRB mechanisms and urging revised disinfection to mitigate ARG spread.},
}

*Chlorine/pharmacology
*Gene Transfer, Horizontal/drug effects
*Drug Resistance, Microbial/genetics
Water Microbiology
Disinfectants/pharmacology
*Bacteria/genetics/drug effects
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Microbial Sensitivity Tests

@article {pmid40950580,
year = {2025},
author = {Panteleev, V and Kulbachinskiy, A and Gelfenbein, D},
title = {Evaluating phage lytic activity: from plaque assays to single-cell technologies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659093},
pmid = {40950580},
issn = {1664-302X},
abstract = {Bacteriophages are the most abundant biological entities on Earth, playing critical roles in microbial ecology, evolution, and horizontal gene transfer. Since the discovery of bacteriophages in the early 20th century, a wide range of techniques has been developed to study their lytic activity. This review provides a perspective on the wide range of methods for studying phage-bacteria interactions, spanning classical bulk-culture techniques and modern single-cell and high-throughput approaches. The first section covers solid culture methods relying on plaque formation phenomenon, which allow for quantification of infectious viruses, phage host-range establishment, and analysis of certain phage traits, now augmented by robotic high-throughput screening. The second section focuses on liquid culture approaches, utilizing optical density measurements, quantitative PCR, metabolic assays and cell damage assays to measure the infection dynamics. The third section details single-cell techniques, which help to dissect the heterogeneity of infection within cell populations, using microscopy, microfluidics, next-generation sequencing, and Hi-C methods. The integration of these diverse methods has greatly advanced our understanding of the molecular mechanisms of phage infection, bacterial immunity, and facilitated phage therapy development. This review is dedicated to the 110th anniversary of phage discovery and is aimed to guide researchers in selecting optimal techniques in the fast-growing field of phage biology, phage-host interactions, bacterial immunity, and phage therapy.},
}

@article {pmid40950087,
year = {2025},
author = {Moe, R and Piechowiak, KW and Håvarstein, LS and Kjos, M and Straume, D},
title = {LytF contributes to pilus extrusion during natural competence in Streptococcus sanguinis SK36.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.04.674207},
pmid = {40950087},
issn = {2692-8205},
abstract = {UNLABELLED: Streptococci may enter a physiological state called competence, during which they express a specific set of genes required for exogenous DNA uptake and its subsequent integration into the genome through homologous recombination. This process, termed natural transformation, facilitates the horizontal acquisition of genetic material, potentially conferring adaptive advantages that enhance bacterial survival under selective pressures. To make homologous DNA available in the surrounding environment, Streptococcus pneumoniae expresses a cell wall hydrolase (CbpD) that lyses and kills closely related species. This process has been coined fratricide , and the acting hydrolase a fratricin . A significant fraction of streptococcal species does not encode a CbpD-like protein, but another competence-induced peptidoglycan hydrolase LytF. It has been speculated that LytF serves the same purpose as CbpD, however, our investigations into the role of LytF in Streptococcus sanguinis revealed no evidence supporting LytF as a fratricin. Instead, we show that LytF is involved in natural transformation by promoting DNA uptake. An essential part of DNA uptake is the competence-induced type IV pilus, which facilitates DNA uptake by pulling nearby DNA toward the cell. By immunoblotting and microscopy imaging, we found that LytF increases the extracellular levels of the major pilus component ComGC, suggesting that LytF may modify peptidoglycan to promote pilus extrusion across the cell wall, thereby enhancing the efficiency of DNA uptake.

IMPORTANCE: Streptococci are a significant cause of severe infections in both humans and animals. They are particularly adept at acquiring new genes through horizontal gene transfer as they can become competent for natural transformation. This allows them to quickly adapt to selective pressure and spread genes involved in virulence and antibiotic resistance. In Streptococcus sanguinis , the competence-induced peptidoglycan hydrolase LytF has been reported to stimulate natural transformation. Our study adds to the understanding of this process by demonstrating that LytF promotes extrusion of the transformation pilus required for DNA uptake.},
}

@article {pmid40950011,
year = {2025},
author = {Yang, B and Xiang, C and Li, T and Liu, B and Sinitskiy, AV and Li, J},
title = {Evolutionary Tree in Chemical Space of Natural Products.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.31.673394},
pmid = {40950011},
issn = {2692-8205},
abstract = {Natural products (NPs) are key to biological function and adaptation, with their distribution shaped by complex evolutionary and ecological forces. While it may seem reasonable to assume that closely related species produce chemically similar NPs, this assumption has not been systematically tested at a broad taxonomic scale. Here, we evaluate whether evolutionary (taxonomic) proximity correlates with chemical similarity in large-scale data from the Lotus database of NPs. We use five deep learning-based encoders, including Chemformer and SMILES Transformer, to embed NPs into a high-dimensional "chemical space." Our results demonstrate that, for flowering plants (Magnoliopsida) and conifers (Pinopsida), species separated by shorter taxonomic distances tend to produce significantly more similar NPs. Similar trends are observed for Fungi and Metazoa, albeit with some complications, possibly due to horizontal gene transfer, convergent evolution, and/or incomplete coverage in the dataset used for NPs. Our findings suggest that the evolutionary tree can be statistically recovered in a chemical space of NPs, provided that this space is constructed with appropriate deep learning techniques, and provide a new computational framework to investigate the evolutionary dynamics of secondary metabolism. These results can inform drug design strategies, for example by enabling the reconstruction of NPs from poorly studied or extinct species.},
}

@article {pmid40946852,
year = {2025},
author = {Zheng, C and Song, J and Shan, M and Qiu, M and Cui, M and Huang, C and Chen, W and Wang, J and Zhang, L and Yu, Y and Fang, H},
title = {Nutrition cycling microbiomes drive the succession of antibiotic resistome in long-term manured soils.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.09.019},
pmid = {40946852},
issn = {2090-1224},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes (ARGs) in the environment has received widespread attention. Nutrition cycling microbiomes specifically refer to microorganisms capable of mineralizing nitrogen and phosphorus, which dominate the microbial community in long-term manured soils. However, changes in nutrition cycling genes/microbiomes and the mechanisms by which these microbiomes mediate ARG transfer through vertical and horizontal gene transfer remain poorly understood.

OBJECTIVES: This study aimed to elucidate how nutrition cycling microbiomes mediate the dissemination and ecological risk of antibiotic resistance genes (ARGs) in long-term manure-amended soils.

METHODS: Here, we employed metagenomic assembly and binning to investigate the distribution of nutrition mineralization genes, nutrition cycling microbiomes, mobile genetic elements (MGEs), and ARGs in rapeseed cake, pig manure, duck manure and their corresponding long-term amended soils.

RESULTS: Long-term application of organic manures led to the dominance of nutrition cycling microbiomes associated with methanogenesis (pmoA and mmoX) and incomplete denitrification (norBC), thereby exacerbating soil nutrient loss. Nutrition cycling microbiomes, particularly Rhodanobacter and Pseudomonas, served as the primary host for ARGs and harbored multiple clinically relevant resistance genes, including MexF, ceoB, and mdtB. Notably, the abundance of ARGs in rapeseed cake and pig manure was 2.09-2.23-fold and 6.74-7.38-fold higher, respectively, than in duck manure, promoting the vertical transmission of ARGs via nutrition cycling microbiomes under long-term application. Furthermore, a significant positive correlation between nutrition mineralization genes and ARGs revealed a co-dispersal mechanism between nutrition cycling microbiomes and ARGs in long-term manured soils.

CONCLUSIONS: It is concluded that the nutrition cycling microbiome plays a more prominent role in shaping antibiotic resistome through vertical transfer in manured soils, compared to horizontal gene transfer mediated by MGEs.},
}

@article {pmid40946639,
year = {2025},
author = {Chen, H and Cheng, D and Sun, M and Zhao, S and Sheng, J and Yu, X and Li, X and Xue, G and Zou, X},
title = {Fe[0] drives tetracycline resistance genes reduction and resistance mechanism shift in activated sludge system.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127302},
doi = {10.1016/j.jenvman.2025.127302},
pmid = {40946639},
issn = {1095-8630},
abstract = {The proliferation of tetracycline antibiotic resistance genes (TC-ARGs) in wastewater treatment plants (WWTPs) poses environmental and health risks. This study investigates zero-valent iron (Fe[0]) in regulating TC-ARGs in activated sludge under co-exposure with tetracycline (TC). TC enriched tetA and tetC via efflux pump activation and horizontal gene transfer (HGT), with tetA/tetC increasing 0.19-3.57 log units and intI1 by 1-2 log units. Fe[0] addition slightly affected absolute TC-ARGs abundance in the first 40 d, with a 4.02 % decrease after 40 d, while relative abundance dropped markedly by 77.81 % and 84.87 % in the first and last 40 d, respectively; intI1 relative abundance decreased by 78.28 %. Fe[0] shifted resistance from efflux genes toward ribosomal protection (tetM/O) and enzymatic modification (tetX), reduced bioavailable TC by 39.8 %, and alleviated EPS inhibition by enhancing polysaccharide production, weakening antibiotic selection pressure. Microbial community restructuring enriched stress-tolerant taxa (e.g., Bacteroidetes). This study demonstrates that Fe[0] primarily reduces the dissemination risk of TC-ARGs by lowering their proportion in microbial genomes. These results provide new insights into optimizing the application of Fe[0] for controlling the spread of TC-ARGs in WWTPs.},
}

@article {pmid40945797,
year = {2025},
author = {Cui, L and Gao, M and Chen, J and Yan, Y and Guo, S and Ma, Y},
title = {How microbial consortium-based compound enzyme influences conjugative transfer pathway of antibiotic resistance genes?.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133305},
doi = {10.1016/j.biortech.2025.133305},
pmid = {40945797},
issn = {1873-2976},
abstract = {Microbial consortium-based compound enzyme (MCE) has been proved to be able to effectively reduce the risk of antibiotic resistance genes (ARGs) dissemination during biotransformation of food waste. However, in-depth mechanisms regarding the regulation of ARGs transfer among environmental bacteria by MCE pretreatment is remain unclear. This work analyzed the effect of MCE pretreatment on RP4 plasmid-mediated conjugative transfer of ARGs and relevant underlying mechanisms. Results showed that MCE pretreatment reduced the plasmid conjugative transfer frequency by 71% compared with the control. Meanwhile, the reduction of hydrophilic components of extracellular polymeric substances, the decrease of biofilm formation, and the disruption of intercellular contact also happened during MCE pretreatment process. In addition, ATP synthesis and bacterial motility had an effect on the plasmid replication and formation of conjugative transfer channel. These changes lead to down-regulation of the expression of conjugative transfer gene. The inhibitory effect of MCE pretreatment on plasmid conjugative transfer was confirmed in the constructed food waste model. MCE pretreatment reduced the number of pathogens, such as Escherichia-Shigella and Rothia, thereby reduced the potential risk of ARGs being disseminated among pathogens. Overall, this study reveals the key mechanism of MCE pretreatment on disrupting ARGs conjugative transfer, which may provide a crucial theoretical foundation for developing novel interventions to disrupt the environmental dissemination of ARGs in future.},
}

@article {pmid40945439,
year = {2025},
author = {Wang, W and Yang, W and Jiang, L and Yao, C and Zhang, Z and Xu, M and Yan, X and Qian, X},
title = {Applications of Oxford Nanopore Technology in the analysis of antibiotic resistance genes: A review.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139824},
doi = {10.1016/j.jhazmat.2025.139824},
pmid = {40945439},
issn = {1873-3336},
abstract = {Antibiotic misuse has led to the rapid expansion of the antibiotic resistance gene (ARGs) pool, making antimicrobial resistance (AMR) a major global health threat. The efficient identification of ARGs and the development of strategies to control AMR have become research hotspots. However, the Next-generation sequencing (NGS) has many limitations in ARGs identification, hindering our understanding of their genetic context. This review uses Oxford Nanopore Technology (ONT) as an example to summarize the advantages and application prospects of the third-generation sequencing technologies in the migration and transmission of ARGs. By analyzing 12 sets of NGS - ONT datasets, this review demonstrates the strengths and limitations of ONT from multiple perspectives, including the identification of ARGs, key pathogens, plasmids, viruses, and horizontal gene transfer events, and provides detailed analytical workflows. It offers comprehensive analytical approaches and application insights for ARGs research based on ONT, highlighting the importance and necessity of the third-generation sequencing technologies in studying the prevalence and transmission of ARGs in complex environments.},
}

@article {pmid40943202,
year = {2025},
author = {Pruss, A and Kobylińska, D and Fijałkowski, K and Masiuk, H and Kwiatkowski, P},
title = {Evaluation of Colistin Susceptibility of Klebsiella pneumoniae Strains Exposed to Rotating Magnetic Field.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178281},
pmid = {40943202},
issn = {1422-0067},
abstract = {Klebsiella pneumoniae, due to its capacity to produce numerous virulence factors and form biofilms, is one of the most significant etiological agents of nosocomial infections. The extensive and often unwarranted use of antibiotic therapy has driven the emergence of various mutations, adaptive mechanisms, and horizontal gene transfer among K. pneumoniae strains, resulting in resistance to most beta-lactam antibiotics, carbapenems, and the last-resort drug-colistin. A promising alternative or adjunctive treatment is the application of rotating magnetic fields (RMFs). The present study aimed to evaluate changes in colistin susceptibility among 20 extended-spectrum beta-lactamases (ESBLs) and 20 K. pneumoniae carbapenemase (KPC)-positive K. pneumoniae strains isolated from hospital infections following exposure to RMF at frequencies of 5 and 50 Hz. Exposure to RMF at 5 Hz resulted in decreased colistin minimum inhibitory concentration (MIC) values in over half of the tested (ESBLs) and (KPC)-positive strains. Additionally, RMF at 50 Hz reduced colistin MIC values in 30% of (ESBL)-positive and 40% of (KPC)-positive strains. Therefore, in the future, RMF may be developed as a supportive therapeutic strategy to improve the efficacy of antibiotics in the treatment of infections caused by multidrug-resistant (MDR) pathogens, including colistin-resistant K. pneumoniae.},
}

@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}

@article {pmid40934669,
year = {2025},
author = {Osti, JF and Pereira Leal, RM and de Souza, AJ and Paulon Rezende, LG and Viana, DG and Andreote, FD and Mendonça, RS and Jakelaitis, A and Regitano, JB},
title = {Complex interplay between composted manure application, metal contamination, and antibiotic resistance genes profile under tropical field conditions.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109783},
doi = {10.1016/j.envint.2025.109783},
pmid = {40934669},
issn = {1873-6750},
abstract = {Manure applications in agricultural soils are a major driver of antibiotic resistance gene (ARG) dissemination, yet long-term effects of composted manure applications under tropical real field conditions remain unclear. This study assessed how successive composted manure applications influence soil physicochemical attributes, bacteriome and resistome profiles in the Brazilian Cerrado, including one site with naturally high heavy metal content. Across all sites, multidrug resistance genes were most abundant, followed by macrolide-lincosamide-streptogramin (MLS), tetracycline, β-lactam and glycopeptides resistance, aligning with predominance of Actinomycetota and Pseudomonadota as key ARG hosts. Manure increased soil pH and available phosphorus (P), with pH significantly shaping bacterial communities and pH and P the resistome in uncontaminated sites (2 and 3). However, in the metal-rich site (1), Cu was the dominant driver. Manure increased ARG richness and changed resistome structure but did not affect clinically relevant genes or resistome diversity. Metal resistance genes (MRGs), particularly for Cu and Zn, strongly influenced resistome dynamics, highlighting co-selection. Integrons integrase genes (intl) abundance increased in metal-depleted but not in metal-rich soils. While composting appears to mitigate ARG spread, particularly for clinically relevant genes, the high antibiotic use in livestock, large manure volumes, and potential for ARG persistence in tropical soils highlight the need for further research on manure treatment strategies and ARG fate in these environments. Environmental Implication. Our study highlights the environmental risks of antibiotic resistance gene (ARG) dissemination in tropical agricultural soils, emphasizing the role of manure application and heavy metal contamination in shaping soil resistome. While composted manure increased bacterial diversity and ARG richness, it did not significantly impact clinically relevant genes and resistome diversity, suggesting that composting may help mitigate ARG spread but does not eliminate it. Metals were the dominant drivers of ARG selection in the contaminated site, underscoring the role of co-selection mechanisms in maintaining resistance. However, manure applications increased integrons abundance, raising concerns about horizontal gene transfer and potential ARG proliferation into pathogens. These findings stress the urgent need for improved manure management policies in Brazil, where high antibiotic use in livestock and large manure volumes pose significant environmental and public health risks. Developing sustainable manure treatment strategies and monitoring ARG persistence are essential to limit antibiotic resistance proliferation in tropical agricultural ecosystems.},
}

@article {pmid40933520,
year = {2025},
author = {Habib, I and Mohamed, MI and Lakshmi, GB and Al Marzooqi, HM and Afifi, HS and Shehata, MG and Elbediwi, M},
title = {First detection and genomic analysis of mcr-1-positive Salmonella Infantis isolated from a broiler production system in the United Arab Emirates.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1592955},
doi = {10.3389/fvets.2025.1592955},
pmid = {40933520},
issn = {2297-1769},
abstract = {This study reports the first detection of mcr-1.1-mediated colistin resistance in Salmonella enterica serovar Infantis from a commercial broiler farm in the United Arab Emirates (UAE). Two S. infantis isolates (SAL_93 and SAL_94) were recovered from caecal droppings and characterized using whole-genome sequencing (WGS). Genomic analysis revealed a single-nucleotide polymorphism (SNP) difference between them, confirming their close epidemiological relationship. Both isolates belonged to multilocus sequence type 32 and exhibited multidrug resistance (MDR), including resistance to colistin (MIC = 4 mg/L) and ciprofloxacin (MIC = 0.5 mg/L). Notably, the mcr-1.1 gene was detected on a conjugative IncX4 plasmid. Additionally, the isolates harbored a large (275,043 bp) conjugative IncFIB plasmid carrying multiple AMR genes, including aadA1, sul1, tet(A), qacEdelta1. Bioinformatic analysis showed a high identity for globally reported mcr-1.1-carrying IncX4 plasmids. The investigation of virulence-associated factors in the studied isolates identified 162 potential virulence-related genes. These included genes linked to the type 3 secretion system, specifically those encoded by pathogenicity island-1 (SPI-1). However, multiple genes linked to the second type 3 secretion system, encoded by SPI-2, were absent in all isolates. These findings suggest a potential risk of horizontal gene transfer in poultry production. Given these risks, the UAE's recent ban on colistin in veterinary medicine marks a crucial step in mitigating AMR transmission within a One Health framework.},
}

@article {pmid40933131,
year = {2025},
author = {Braun, SD and Reinicke, M and Diezel, C and Müller, E and Frankenfeld, K and Schumacher, T and Arends, H and Monecke, S and Ehricht, R},
title = {High-throughput screening of monoclonal antibodies against carbapenemases using a multiplex protein microarray platform.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650094},
doi = {10.3389/fmicb.2025.1650094},
pmid = {40933131},
issn = {1664-302X},
abstract = {INTRODUCTION: Carbapenemase-producing bacteria undermine the efficacy of carbapenems, a class of last-resort antibiotics used primarily to treat infections caused by multidrug-resistant Gram-negative pathogens. Carbapenemases are among the most alarming antimicrobial resistance mechanisms because they inactivate all β-lactam antibiotics leaving clinicians with few or no therapeutic options. The genes encoding these enzymes are typically located on mobile genetic elements (MGE), which facilitate rapid horizontal gene transfer among different bacterial species. These MGE's often additionally carry toxin-antitoxin systems that promote long-term persistence in bacterial populations. Carbapenem-resistant Enterobacteriaceae (CRE) often colonize the gastrointestinal tract without symptoms, serving as silent reservoirs for further dissemination. Infections caused by CRE are associated with high morbidity and mortality and are frequently resistant to multiple drug classes. Given the urgent clinical need for rapid diagnostics, immunochromatographic assays represent a promising and urgently needed approach for economic and available point-of-care detection. However, the development of such assays is often hindered by the time-consuming process of identifying high-affinity antibody pairs.

METHODS: To accelerate this process, we evaluated a protein microarray platform as a high-throughput screening tool to identify optimal monoclonal antibody (mAb) pairs targeting the most clinically relevant carbapenemases. Monoclonal antibodies derived from hybridoma libraries and commercial sources were spotted in triplicates and tested in a single experiment against lysates from reference strains expressing the carbapenemase enzymes KPC, NDM, IMP, VIM, OXA-23/48/58, and MCR-1, an enzyme conferring resistance to colistin. Signal intensities were quantified, and diagnostic performance was assessed across four thresholds.

RESULTS: A cut-off > 0.2 yielded the best balance, with approximately 61% balanced accuracy and ≥99% specificity. Around 22% of tested antibodies showed strong, reproducible reactivity. For several targets-such as KPC, IMP, VIM, OXA-58, and MCR-1-100% sensitivity was achieved. The array allowed simultaneous mapping of cross-reactivity, a key advantage over conventional ELISA workflows.

DISCUSSION: Our findings confirm that protein-based microarrays offer a robust, efficient platform for antibody pair selection, reducing reagent use while accelerating assay development. The validated antibody pairs are directly applicable to ELISA or lateral flow test formats and provide a strong foundation for next-generation diagnostics capable of detecting an evolving panel of carbapenemases in clinical settings.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929971,
year = {2025},
author = {Wang, Y and Han, Y and Li, L and Liu, J and Tian, H},
title = {Airborne human-associated ARGs in municipal wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139766},
doi = {10.1016/j.jhazmat.2025.139766},
pmid = {40929971},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) in bioaerosols pose significant health hazards to humans because of their inhalability. Municipal wastewater treatment plants (MWTPs) are one of the typical sources of bioaerosol generation. However, there is a lack of clear understanding of human-associated ARGs (HA-ARGs) in bioaerosols from MWTPs. This study focused on airborne HA-ARGs in a typical MWTP. The results found that 331 HA-ARGs were identified in bioaerosols, dominated by multidrug, aminoglycoside, β-lactam, macrolide, lincosamide, and streptogramin genes. The detected abundances of the airborne HA-ARGs were 5.77-2.12E+ 03 transcripts per kilobase million (TPM), 202.36-3.17E+ 09 copies/ngDNA, and 4.42-4.92E+ 06 copies/m[3]air. The greatest abundances were detected mainly in the sludge dewatering house and in the summer and winter. HA-ARGs were mainly propagated and amplified by vertical gene transfer (VGT) and horizontal gene transfer (HGT). Proteobacteria, Actinobacteria, and Bacteroidetes were bacteria that had a strong co-occurrence with airborne HA-ARGs in VGT. Plasmids and transposases were the dominant mobile genetic elements in HGT. The analysis of co-occurrence network showed that VGT was identified as the main pathway for the spread and amplification of airborne HA-ARGs, with an average contribution of 85.38 %. These results provide a theoretical basis for potential risk assessment and reduction of airborne HA-ARGs in MWTPs.},
}

@article {pmid40929802,
year = {2025},
author = {Yang, KY and Sun, YF and Liang, YS and Li, H and Qi, MX and Wang, Z and Ramos Aguila, LC and Cai, LQ and Li, HS and Pang, H},
title = {Horizontally transferred NADAR genes contribute to immune defense of ladybird beetles against bacterial infection.},
journal = {Insect biochemistry and molecular biology},
volume = {184},
number = {},
pages = {104397},
doi = {10.1016/j.ibmb.2025.104397},
pmid = {40929802},
issn = {1879-0240},
abstract = {Horizontal gene transfer (HGT) is now widely recognized as an important mechanism contributing to host immunity and adaptation. Ladybird beetles, with their diverse diets and habitats, encounter a broad spectrum of microbial threats, making effective immune responses critical for their survival. However, the immune roles of HGT-acquired genes in ladybirds remain largely unexplored. To address this gap, we investigated HGT of a NADAR (NAD- and ADP-ribose-associated) domain-containing gene from microorganisms to insects. Phylogenetic analyses revealed that NADAR genes in ladybird beetles form a well-supported clade nested within a larger group composed primarily of bacterial sequences, providing strong evidence for an HGT origin. Sampling across 69 ladybird species suggests that NADAR genes originated in the Coccinellidae family and were subsequently retained or duplicated across ladybird genomes, indicating their functional importance. Using the ladybird Cryptolaemus montrouzieri as a model, we observed that the expression levels of CmNADAR1 and CmNADAR2 were significantly upregulated in response to bacterial infection. Immune challenges combined with RNA interference targeting NADAR genes led to reduced survival rates and marked necrosis in intestinal tissues, compared to controls exposed to either bacterial infection or dsRNA alone. Together, our results demonstrate that NADAR genes in ladybird beetles were acquired through horizontal gene transfer and contribute to immune defense against bacterial infection.},
}

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40928248,
year = {2025},
author = {Hourigan, D and Field, D and Murray, E and Sugrue, I and O'Connor, PM and Hill, C and Ross, RP},
title = {Nisin-like biosynthetic gene clusters are widely distributed across microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0154525},
doi = {10.1128/mbio.01545-25},
pmid = {40928248},
issn = {2150-7511},
abstract = {Bacteriocins are antimicrobial peptides/proteins that can have narrow or broad inhibitory spectra and remarkable potency against clinically relevant pathogens. One such bacteriocin that is extensively used in the food industry and with potential for biotherapeutic application is the post-translationally modified peptide, nisin. Recent studies have shown the impact of nisin on the gastrointestinal microbiome, but relatively little is known of how abundant nisin production is in nature, the breadth of existing variants, and their antimicrobial potency. Whether or not nisin production and immunity are widespread in gut microbiomes could be a deciding factor in determining the suitability of nisin as a prospective therapeutic for human and/or animal infections. Here, we used publicly available data sets to determine the presence of widespread and diverse nisin biosynthetic gene clusters (nBGCs) across the biosphere. We show that 30% of these nBGCs are predicted to be located on mobile genetic elements, with some found in pathogenic bacteria. Furthermore, we highlight evidence of horizontal gene transfer of nBGCs between genera, including Streptococcus suis, Enterococcus hirae, and Staphylococcus aureus. In all, we describe 107 novel nisin-like peptides. Five representatives were heterologously expressed and all exhibited antimicrobial activity. We further characterized nisin VP, a novel natural nisin variant produced by Velocimicrobium porci isolated from the porcine gut. The peptide has a completely novel hinge region "AIQ" not detected in other nisin variants to date. While nisin VP could be induced by nisin A, the latter could not be induced by nisin VP.IMPORTANCEOur research reveals the heretofore underappreciated presence of diverse and widespread nisin-like biosynthetic gene clusters in microbiomes across the globe. Notably, different clusters share similar biosynthetic machinery but differ in sequence, suggesting gene transfer and adaptation. We identify >100 new nisin-like variants, including several in species not previously known to produce nisin. This emphasizes the widespread dissemination of nisin-like gene clusters and the diversity of novel core peptides with biotherapeutic potential. These findings point to a role for nisin in microbial competition in microbiomes. We heterologously expressed nine nisin variants, five of which are completely novel peptides, using the nisin A biosynthetic machinery and confirmed that all exhibited antimicrobial activity.},
}

@article {pmid40927181,
year = {2025},
author = {Ziemann, M and Mitrofanov, A and Stöckl, R and Alkhnbashi, OS and Backofen, R and Hess, WR},
title = {Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqaf020},
pmid = {40927181},
issn = {2633-6693},
abstract = {Clustered regularly interspaced palindromic repeats (CRISPR)-associated transposons (CAST) consist of an integration between certain class 1 or class 2 CRISPR-Cas systems and Tn7-like transposons. Class 2 type V-K CAST systems are restricted to cyanobacteria. Here, we identified a unique subgroup of type V-K systems through phylogenetic analysis, classified as V-K_V2. Subgroup V-K_V2 CAST systems are characterized by an alternative tracrRNA, the exclusive use of Arc_2-type transcriptional regulators, and distinct differences in the length of protein domains in TnsB and TnsC. Although the occurrence of V-K_V2 CAST systems is restricted to Nostocales cyanobacteria, it shows signs of horizontal gene transfer, indicating its capability for genetic mobility. The predicted V-K_V2 tracrRNA secondary structure has been integrated into an updated version of the CRISPRtracrRNA program available on GitHub under https://github.com/BackofenLab/CRISPRtracrRNA/releases/tag/2.0.},
}

@article {pmid40925947,
year = {2025},
author = {Smyth, C and Leigh, RJ and Do, TT and Walsh, F},
title = {Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {78},
pmid = {40925947},
issn = {2731-8745},
support = {Grant 2019-W-PhD-14//Irish Environmental Protection Agency/ ; Grant 2019-W-PhD-14//Irish Environmental Protection Agency/ ; PHD_3//The Kathleen Lonsdale Institute for Human Health Research, Maynooth University/ ; PHD_3//The Kathleen Lonsdale Institute for Human Health Research, Maynooth University/ ; },
abstract = {Plasmids facilitate antimicrobial resistance (AMR) gene spread via horizontal gene transfer, yet the mobility of genes in wastewater treatment plant (WWTP) resistomes remains unclear. We sequenced 173 circularised plasmids transferred from WWTP effluent into Escherichia coli and characterised their genetic content. Multiple multidrug-resistant plasmids were identified, with a significant number of mega-plasmids (>100 kb). Almost all plasmids detected existed with other plasmids i.e. as communities rather than lone entities. These plasmid communities enabled non-AMR plasmids to survive antimicrobial selection by co-existing with resistant partners. Our data demonstrates the highly variable nature of plasmids in addition to their capacity to carry mobile elements and genes within these highly variable regions. The impact of these variations on plasmid ecology, persistence, and transfer requires further investigation. Plasmid communities warrant exploration across biomes, as many non-resistant plasmids escape elimination by co-existing with AMR plasmids in the same bacterial host, representing a previously unrecognised survival strategy.},
}

@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {16},
number = {9},
pages = {e0113425},
doi = {10.1128/mbio.01134-25},
pmid = {40793781},
issn = {2150-7511},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; },
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*DNA Transposable Elements
Feces/microbiology
Ecuador
Metagenomics
Child
Child, Preschool
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Female
Gene Transfer, Horizontal
Male
Plasmids/genetics

@article {pmid40923893,
year = {2025},
author = {Reyes Gamas, K and Seamons, TR and Dysart, MJ and Fang, L and Chappell, J and Stadler, LB and Silberg, JJ},
title = {Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00313},
pmid = {40923893},
issn = {2161-5063},
abstract = {Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNAs that store information within user-defined sets of microbes in environmental communities for gene transfer studies.},
}

@article {pmid40919919,
year = {2025},
author = {Luo, Y and Srinivas, A and Guidry, C and Bull, C and Haney, CH and Hamilton, C},
title = {GacA regulates symbiosis and mediates lifestyle transitions in Pseudomonas.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0027725},
doi = {10.1128/msphere.00277-25},
pmid = {40919919},
issn = {2379-5042},
abstract = {Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the brassicacearum/corrugata/mediterranea (BCM) subclade of Pseudomonas fluorescens, including Pseudomonas species N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. Pseudomonas sp. N2E2 is a plant commensal and contains genes encoding biosynthetic enzymes for the antifungal compound 2,4-diacetylphloroglucinol (DAPG). In contrast, Pseudomonas sp. N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)- and syringopeptin (SYP)-like toxins from the plant pathogen Pseudomonas syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant-pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle. Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.IMPORTANCEEmerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer (HGT) aids in the acquisition of novel genes that facilitate adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT. These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. This work provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.},
}

@article {pmid40916842,
year = {2025},
author = {Oo, G and Low, WW and Yong, M and Stanton, TD and Ayuni, NN and Bifani, P and Wyres, KL and Gan, YH},
title = {Anti-plasmid defense in hypervirulent Klebsiella pneumoniae involves Type I-like and Type IV restriction modification systems.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2558877},
doi = {10.1080/22221751.2025.2558877},
pmid = {40916842},
issn = {2222-1751},
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.},
}

@article {pmid40914064,
year = {2025},
author = {Zhang, K and Gao, J and Zhang, J and Wang, Y and Wang, H and Guo, Y and Lu, T},
title = {Preservatives induced succession of microbial communities and proliferation of resistance genes within biofilm and plastisphere in sulfur autotrophic denitrification system.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139750},
doi = {10.1016/j.jhazmat.2025.139750},
pmid = {40914064},
issn = {1873-3336},
abstract = {Methylparaben (MeP), Benzethonium chloride (BZC) and microplastics (MPs) as emerging contaminants are frequently detected in the environment. Furthermore, MPs can be colonized by microorganisms to form a unique ecological niche known as the "plastisphere". In this study, three biofilm-based sulfur autotrophic denitrification (SAD) reactors were established, which were exposed to 0.5-5 mg/L MeP and BZC individually and in combination, while polyamide 6 bags were added to cultivate plastisphere within the three SAD systems. The results found that BZC had a more serious inhibition effect than MeP. Besides, MeP mitigated the toxicity of BZC on SAD, and the observed inhibition gradually diminished over time. The incorporation of preservatives significantly changed the microbial community structures and induced the proliferation of resistance genes (RGs) in both biofilm and plastisphere. Enrichment of functional bacterium like Thiobacillus and the colonization of pathogenic bacterium like Desulfovibrio were found in plastisphere. The proliferation of intracellular RGs in biofilm might drive the recovery of SAD performance. In addition, mobile genetic elements were recognized as the key drivers of horizontal gene transfer responsible for the dissemination of RGs. This research guided the efforts to control the risks associated with preservatives and MPs in wastewater treatment.},
}

@article {pmid40904109,
year = {2025},
author = {Clabby, T and Tesson, F and Gaborieau, B and Bernheim, A},
title = {Why do bacteria accumulate antiphage defence systems?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240082},
pmid = {40904109},
issn = {1471-2970},
support = {//MSDAVENIR/ ; //Pasteur Institute/ ; /ERC_/European Research Council/International ; },
mesh = {*Bacteria/classification/genetics/immunology/virology ; *Bacteriophages/genetics/physiology ; Ecology ; CRISPR-Cas Systems ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Phage Therapy ; },
abstract = {While it is well established that bacterial genomes encode multiple and diverse antiphage systems, the reasons for their co-occurrence and their heterogeneous distribution remain debated. This review examines why bacteria accumulate antiphage systems and how this influences phage-bacteria interactions, particularly in the context of phage therapy. Two main hypotheses may explain this phenomenon: (i) the pan-immunity hypothesis, which suggests that defence system accumulation provides protection against phage predation at the community level, and (ii) mobile genetic element (MGE) competition, where defence systems primarily protect intra-bacterial MGEs against other ones rather than the bacterial host itself. The ecological context also influences the distribution of antiphage systems, with defencee accumulation shaping phage-bacteria interactions in diverse communities but playing a lesser role at the species level, potentially explaining why multiple defences do not strongly limit phage host range in therapeutic settings. Finally, we address the challenges in understanding the drivers shaping the distribution of defence systems across bacterial genomes (expressions, costs, etc.) and their implications for elucidating the ecological role of defence systems and optimizing phage therapy strategies.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}

*Bacteria/classification/genetics/immunology/virology
*Bacteriophages/genetics/physiology
Ecology
CRISPR-Cas Systems
Gene Transfer, Horizontal
Interspersed Repetitive Sequences
*Phage Therapy